Mercurial > repos > galaxyp > custom_pro_db
changeset 11:982fb2cde6c5 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 7115cf54f290b51b6a791f9ae288dd907a31fb0a
author | galaxyp |
---|---|
date | Fri, 13 Jan 2017 12:18:32 -0500 |
parents | ed65d110c1b5 |
children | 2656b09d2046 |
files | COPYING README.md customProDB.R customProDB.xml test-data/exon_anno.RData test-data/ids.RData test-data/procodingseq.RData test-data/proseq.RData test-data/test1.vcf test-data/test1_sort.bam test-data/test1_sort.bam.bai test-data/test_indel.fasta test-data/test_rpkm.fasta test-data/test_snv.fasta tool-data/customProDB.loc.sample tool_data_table_conf.xml.sample |
diffstat | 4 files changed, 323 insertions(+), 317 deletions(-) [+] |
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line diff
--- a/customProDB.R Wed Jun 08 15:02:58 2016 -0400 +++ b/customProDB.R Fri Jan 13 12:18:32 2017 -0500 @@ -1,113 +1,113 @@ -#!/usr/bin/env Rscript - -initial.options <- commandArgs(trailingOnly = FALSE) -script_parent_dir <- dirname(sub("--file=", "", initial.options[grep("--file=", initial.options)])) - -## begin warning handler -withCallingHandlers({ - -library(methods) # Because Rscript does not always do this - -options('useFancyQuotes' = FALSE) - -suppressPackageStartupMessages(library("optparse")) -suppressPackageStartupMessages(library("RGalaxy")) - - -option_list <- list() - -option_list$bam <- make_option('--bam', type='character') -option_list$bai <- make_option('--bai', type='character') -option_list$vcf <- make_option('--vcf', type='character') -option_list$exon_anno <- make_option('--exon_anno', type='character') -option_list$proteinseq <- make_option('--proteinseq', type='character') -option_list$procodingseq <- make_option('--procodingseq', type='character') -option_list$ids <- make_option('--ids', type='character') -option_list$dbsnpinCoding <- make_option('--dbsnpinCoding', type='character') -option_list$cosmic <- make_option('--cosmic', type='character') -option_list$annotationFromHistory <- make_option('--annotationFromHistory', type='logical', action="store_true", default=FALSE) -option_list$rpkmCutoff <- make_option('--rpkmCutoff', type='character') -#option_list$outputIndels <- make_option('--outputIndels', type='logical', action="store_true", default=FALSE) -#option_list$outputNovelJunctions <- make_option('--outputNovelJunctions', type='logical', action="store_true", default=FALSE) -option_list$outputFile <- make_option('--outputFile', type='character') - - -opt <- parse_args(OptionParser(option_list=option_list)) - - -customProDB <- function( - bam_file = GalaxyInputFile(required=TRUE), - bai_file = GalaxyInputFile(required=TRUE), - vcf_file = GalaxyInputFile(required=TRUE), - exon_anno_file = GalaxyInputFile(required=TRUE), - proteinseq_file = GalaxyInputFile(required=TRUE), - procodingseq_file = GalaxyInputFile(required=TRUE), - ids_file = GalaxyInputFile(required=TRUE), - dbsnpinCoding_file = GalaxyInputFile(required=FALSE), - cosmic_file = GalaxyInputFile(required=FALSE), - annotationFromHistory = GalaxyLogicalParam(required=FALSE), - rpkmCutoff = GalaxyNumericParam(required=TRUE), - #outputIndels = GalaxyLogicalParam(required=FALSE), - #outputNovelJunctions = GalaxyLogicalParam(required=FALSE), - outputFile = GalaxyOutput("FASTA","fasta")) -{ - file.symlink(exon_anno_file, paste(getwd(), "exon_anno.RData", sep="/")) - file.symlink(proteinseq_file, paste(getwd(), "proseq.RData", sep="/")) - file.symlink(procodingseq_file, paste(getwd(), "procodingseq.RData", sep="/")) - file.symlink(ids_file, paste(getwd(), "ids.RData", sep="/")) - - if (length(dbsnpinCoding_file) > 0) - { - file.symlink(dbsnpinCoding_file, paste(getwd(), "dbsnpinCoding.RData", sep="/")) - labelrsid = T - } - else - { - labelrsid = F - } - - if (length(cosmic_file) > 0) - { - file.symlink(cosmic_file, paste(getwd(), "cosmic.RData", sep="/")) - cosmic = T - } - else - { - cosmic = F - } - - bamLink = "input.bam" - file.symlink(bam_file, bamLink) - file.symlink(bai_file, paste(bamLink, ".bai", sep="")) - - suppressPackageStartupMessages(library(customProDB)) - - easyRun(bamFile=bamLink, vcfFile=vcf_file, annotation_path=getwd(), - rpkm_cutoff=rpkmCutoff, outfile_path=".", outfile_name="output", - nov_junction=F, INDEL=T, lablersid=labelrsid, COSMIC=cosmic) -} - - -params <- list() -for(param in names(opt)) -{ - if (!param == "help") - params[param] <- opt[param] -} - -setClass("GalaxyRemoteError", contains="character") -wrappedFunction <- function(f) -{ - tryCatch(do.call(f, params), - error=function(e) new("GalaxyRemoteError", conditionMessage(e))) -} - - -suppressPackageStartupMessages(library(RGalaxy)) -do.call(customProDB, params) - -## end warning handler -}, warning = function(w) { - cat(paste("Warning:", conditionMessage(w), "\n")) - invokeRestart("muffleWarning") -}) +#!/usr/bin/env Rscript + +initial.options <- commandArgs(trailingOnly = FALSE) +script_parent_dir <- dirname(sub("--file=", "", initial.options[grep("--file=", initial.options)])) + +## begin warning handler +withCallingHandlers({ + +library(methods) # Because Rscript does not always do this + +options('useFancyQuotes' = FALSE) + +suppressPackageStartupMessages(library("optparse")) +suppressPackageStartupMessages(library("RGalaxy")) + + +option_list <- list() + +option_list$bam <- make_option('--bam', type='character') +option_list$bai <- make_option('--bai', type='character') +option_list$vcf <- make_option('--vcf', type='character') +option_list$exon_anno <- make_option('--exon_anno', type='character') +option_list$proteinseq <- make_option('--proteinseq', type='character') +option_list$procodingseq <- make_option('--procodingseq', type='character') +option_list$ids <- make_option('--ids', type='character') +option_list$dbsnpinCoding <- make_option('--dbsnpinCoding', type='character') +option_list$cosmic <- make_option('--cosmic', type='character') +option_list$annotationFromHistory <- make_option('--annotationFromHistory', type='logical', action="store_true", default=FALSE) +option_list$rpkmCutoff <- make_option('--rpkmCutoff', type='character') +#option_list$outputIndels <- make_option('--outputIndels', type='logical', action="store_true", default=FALSE) +#option_list$outputNovelJunctions <- make_option('--outputNovelJunctions', type='logical', action="store_true", default=FALSE) +option_list$outputFile <- make_option('--outputFile', type='character') + + +opt <- parse_args(OptionParser(option_list=option_list)) + + +customProDB <- function( + bam_file = GalaxyInputFile(required=TRUE), + bai_file = GalaxyInputFile(required=TRUE), + vcf_file = GalaxyInputFile(required=TRUE), + exon_anno_file = GalaxyInputFile(required=TRUE), + proteinseq_file = GalaxyInputFile(required=TRUE), + procodingseq_file = GalaxyInputFile(required=TRUE), + ids_file = GalaxyInputFile(required=TRUE), + dbsnpinCoding_file = GalaxyInputFile(required=FALSE), + cosmic_file = GalaxyInputFile(required=FALSE), + annotationFromHistory = GalaxyLogicalParam(required=FALSE), + rpkmCutoff = GalaxyNumericParam(required=TRUE), + #outputIndels = GalaxyLogicalParam(required=FALSE), + #outputNovelJunctions = GalaxyLogicalParam(required=FALSE), + outputFile = GalaxyOutput("FASTA","fasta")) +{ + file.symlink(exon_anno_file, paste(getwd(), "exon_anno.RData", sep="/")) + file.symlink(proteinseq_file, paste(getwd(), "proseq.RData", sep="/")) + file.symlink(procodingseq_file, paste(getwd(), "procodingseq.RData", sep="/")) + file.symlink(ids_file, paste(getwd(), "ids.RData", sep="/")) + + if (length(dbsnpinCoding_file) > 0) + { + file.symlink(dbsnpinCoding_file, paste(getwd(), "dbsnpinCoding.RData", sep="/")) + labelrsid = T + } + else + { + labelrsid = F + } + + if (length(cosmic_file) > 0) + { + file.symlink(cosmic_file, paste(getwd(), "cosmic.RData", sep="/")) + cosmic = T + } + else + { + cosmic = F + } + + bamLink = "input.bam" + file.symlink(bam_file, bamLink) + file.symlink(bai_file, paste(bamLink, ".bai", sep="")) + + suppressPackageStartupMessages(library(customProDB)) + + easyRun(bamFile=bamLink, vcfFile=vcf_file, annotation_path=getwd(), + rpkm_cutoff=rpkmCutoff, outfile_path=".", outfile_name="output", + nov_junction=F, INDEL=T, lablersid=labelrsid, COSMIC=cosmic) +} + + +params <- list() +for(param in names(opt)) +{ + if (!param == "help") + params[param] <- opt[param] +} + +setClass("GalaxyRemoteError", contains="character") +wrappedFunction <- function(f) +{ + tryCatch(do.call(f, params), + error=function(e) new("GalaxyRemoteError", conditionMessage(e))) +} + + +suppressPackageStartupMessages(library(RGalaxy)) +do.call(customProDB, params) + +## end warning handler +}, warning = function(w) { + cat(paste("Warning:", conditionMessage(w), "\n")) + invokeRestart("muffleWarning") +})
--- a/customProDB.xml Wed Jun 08 15:02:58 2016 -0400 +++ b/customProDB.xml Fri Jan 13 12:18:32 2017 -0500 @@ -1,110 +1,116 @@ -<tool id="custom_pro_db" name="CustomProDB" version="1.10.0"> - <description>Generate protein FASTAs from exosome or transcriptome data</description> - <stdio> - <exit_code range="1:" level="fatal" description="Job Failed" /> - </stdio> - <command interpreter="Rscript --vanilla">customProDB.R - - --bam="$genome_annotation.bamInput" - --bai="${genome_annotation.bamInput.metadata.bam_index}" - --vcf="$genome_annotation.vcfInput" - --rpkmCutoff=$rpkmCutoff - --outputFile="${output_rpkm}" - - #if str($genome_annotation.source) == "history": - --exon_anno="$genome_annotation.exonAnno" - --proteinseq="$genome_annotation.proteinSeq" - --procodingseq="$genome_annotation.proCodingSeq" - --ids="$genome_annotation.ids" - #if str($genome_annotation.dbsnpInCoding) != "None": - --dbsnpinCoding="$genome_annotation.dbsnpInCoding" - #end if - #if str($genome_annotation.cosmic) != "None": - --cosmic="$genome_annotation.cosmic" - #end if - #else: - #set index_path = $genome_annotation.builtin.fields.path - --exon_anno="$index_path/exon_anno.RData" - --proteinseq="$index_path/proseq.RData" - --procodingseq="$index_path/procodingseq.RData" - --ids="$index_path/ids.RData" - #if $genome_annotation.dbsnpInCoding: - --dbsnpinCoding="$index_path/dbsnpinCoding.RData" - #end if - #if $genome_annotation.cosmic: - --cosmic="$index_path/cosmic.RData" - #end if - #end if - -2>&1</command> - <inputs> - <conditional name="genome_annotation"> - <param name="source" type="select" label="Will you select a genome annotation from your history or use a built-in annotation?" help="See `Annotations` section of help below"> - <option value="builtin">Use a built-in genome annotation</option> - <option value="history">Use annotation from your history</option> - </param> - <when value="builtin"> - <param name="builtin" type="select" label="Select genome annotation" help="If your genome of interest is not listed, contact the Galaxy team"> - <options from_data_table="customProDB"> - <filter type="sort_by" column="2"/> - <validator type="no_options" message="No annotations are available for the selected input dataset"/> - </options> - </param> - <param name="bamInput" type="data" format="bam" label="BAM file"> - <validator type="unspecified_build" /> - <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="customProDB" type="dataset_metadata_in_data_table" /> - </param> - <!--<param name="baiInput" type="data" format="bam_index" label="BAM Index (BAI) file"> - <validator type="unspecified_build" /> - <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="customProDB" type="dataset_metadata_in_data_table" /> - </param>--> - <param name="vcfInput" type="data" format="vcf" label="VCF file"> - <validator type="unspecified_build" /> - <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="customProDB" type="dataset_metadata_in_data_table" /> - </param> - <param name="dbsnpInCoding" type="boolean" value="" label="Annotate SNPs with rsid from dbSNP (select organisms only)" /> - <param name="cosmic" type="boolean" value="" label="Annotate somatic SNPs from COSMIC (human only)" /> - </when> - <when value="history"> - <param name="exonAnno" type="data" format="RData" metadata_name="dbkey" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" /> - <param name="proteinSeq" type="data" format="RData" metadata_name="dbkey" help="A dataframe containing protein ids and protein sequences in an RData file" label="Protein Sequences" /> - <param name="proCodingSeq" type="data" format="RData" metadata_name="dbkey" help="A dataframe cotaining coding sequences for each protein in an RData file" label="Protein Coding Sequences" /> - <param name="ids" type="data" format="RData" metadata_name="dbkey" help="A dataframe cotaining IDs for each protein in an RData file" label="Protein IDs" /> - <param name="bamInput" type="data" format="bam" label="BAM file"> - <validator check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" /> - </param> - <param name="baiInput" type="data" format="bam_index" label="BAM Index file"> - <validator check="dbkey" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" /> - </param> - <param name="vcfInput" type="data" format="vcf" label="VCF file" /> - <param name="dbsnpInCoding" type="data" format="RData" label="A dataframe containing dbSNP rsids" optional="true" /> - <param name="cosmic" type="data" format="RData" label="A dataframe containing somatic SNPs from COSMIC (human only)" optional="true" /> - </when> - </conditional> - <param name="rpkmCutoff" type="float" value="1" min="0" label="Transcript Expression Cutoff (RPKM)" help="If non-zero, if a transcript does not meet this expression cutoff (based on RPKM) then it will not be included in the output database." /> - </inputs> - <outputs> - <data format="fasta" name="output_rpkm" from_work_dir="output_rpkm.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_rpkm.fasta"/> - <data format="fasta" name="output_snv" from_work_dir="output_snv.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_snv.fasta"/> - <data format="fasta" name="output_indel" from_work_dir="output_indel.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_indel.fasta"/> - </outputs> - <tests> - <test> - <param name="bamInput" value="test1_sort.bam" dbkey="hg19" /> - <param name="vcfInput" value="test1.vcf" dbkey="hg19" /> - <param name="source" value="history" /> - <param name="exonAnno" value="exon_anno.RData" /> - <param name="proteinSeq" value="proseq.RData" /> - <param name="proCodingSeq" value="procodingseq.RData" /> - <param name="ids" value="ids.RData" /> - <output name="output_rpkm" file="test_rpkm.fasta" /> - <output name="output_snv" file="test_snv.fasta" /> - <output name="output_indel" file="test_indel.fasta" /> - </test> - </tests> - <help> -**Description** - -Generate protein FASTAs from exosome or transcriptome data (in the form of BAM files). -</help> -</tool> \ No newline at end of file +<tool id="custom_pro_db" name="CustomProDB" version="1.10.0"> + <description>Generate protein FASTAs from exosome or transcriptome data</description> + <stdio> + <exit_code range="1:" level="fatal" description="Job Failed" /> + </stdio> + <command interpreter="Rscript --vanilla">customProDB.R + + --bam="$genome_annotation.bamInput" + --bai="${genome_annotation.bamInput.metadata.bam_index}" + --vcf="$genome_annotation.vcfInput" + --rpkmCutoff=$rpkmCutoff + --outputFile="${output_rpkm}" + + #if str($genome_annotation.source) == "history": + --exon_anno="$genome_annotation.exonAnno" + --proteinseq="$genome_annotation.proteinSeq" + --procodingseq="$genome_annotation.proCodingSeq" + --ids="$genome_annotation.ids" + #if str($genome_annotation.dbsnpInCoding) != "None": + --dbsnpinCoding="$genome_annotation.dbsnpInCoding" + #end if + #if str($genome_annotation.cosmic) != "None": + --cosmic="$genome_annotation.cosmic" + #end if + #else: + #set index_path = $genome_annotation.builtin.fields.path + --exon_anno="$index_path/exon_anno.RData" + --proteinseq="$index_path/proseq.RData" + --procodingseq="$index_path/procodingseq.RData" + --ids="$index_path/ids.RData" + #if $genome_annotation.dbsnpInCoding: + --dbsnpinCoding="$index_path/dbsnpinCoding.RData" + #end if + #if $genome_annotation.cosmic: + --cosmic="$index_path/cosmic.RData" + #end if + #end if + +2>&1</command> + <inputs> + <conditional name="genome_annotation"> + <param name="source" type="select" label="Will you select a genome annotation from your history or use a built-in annotation?" help="See `Annotations` section of help below"> + <option value="builtin">Use a built-in genome annotation</option> + <option value="history">Use annotation from your history</option> + </param> + <when value="builtin"> + <param name="builtin" type="select" label="Select genome annotation" help="If your genome of interest is not listed, contact the Galaxy team"> + <options from_data_table="customProDB"> + <filter type="sort_by" column="2"/> + <validator type="no_options" message="No annotations are available for the selected input dataset"/> + </options> + </param> + <param name="bamInput" type="data" format="bam" label="BAM file"> + <validator type="unspecified_build" /> + <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="customProDB" type="dataset_metadata_in_data_table" /> + </param> + <!--<param name="baiInput" type="data" format="bam_index" label="BAM Index (BAI) file"> + <validator type="unspecified_build" /> + <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="customProDB" type="dataset_metadata_in_data_table" /> + </param>--> + <param name="vcfInput" type="data" format="vcf" label="VCF file"> + <validator type="unspecified_build" /> + <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="customProDB" type="dataset_metadata_in_data_table" /> + </param> + <param name="dbsnpInCoding" type="boolean" value="" label="Annotate SNPs with rsid from dbSNP (select organisms only)" /> + <param name="cosmic" type="boolean" value="" label="Annotate somatic SNPs from COSMIC (human only)" /> + </when> + <when value="history"> + <param name="exonAnno" type="data" format="RData" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" /> + <param name="proteinSeq" type="data" format="RData" help="A dataframe containing protein ids and protein sequences in an RData file" label="Protein Sequences" /> + <param name="proCodingSeq" type="data" format="RData" help="A dataframe cotaining coding sequences for each protein in an RData file" label="Protein Coding Sequences" /> + <param name="ids" type="data" format="RData" help="A dataframe cotaining IDs for each protein in an RData file" label="Protein IDs" /> + <param name="bamInput" type="data" format="bam" label="BAM file"> + <validator check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" /> + </param> + <param name="baiInput" type="data" format="bam_index" label="BAM Index file"> + <validator check="dbkey" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" /> + </param> + <param name="vcfInput" type="data" format="vcf" label="VCF file" /> + <param name="dbsnpInCoding" type="data" format="RData" label="A dataframe containing dbSNP rsids" optional="true" /> + <param name="cosmic" type="data" format="RData" label="A dataframe containing somatic SNPs from COSMIC (human only)" optional="true" /> + </when> + </conditional> + <param name="rpkmCutoff" type="float" value="1" min="0" label="Transcript Expression Cutoff (RPKM)" help="If non-zero, if a transcript does not meet this expression cutoff (based on RPKM) then it will not be included in the output database." /> + </inputs> + <outputs> + <data format="fasta" name="output_rpkm" from_work_dir="output_rpkm.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_rpkm.fasta"/> + <data format="fasta" name="output_snv" from_work_dir="output_snv.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_snv.fasta"/> + <data format="fasta" name="output_indel" from_work_dir="output_indel.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_indel.fasta"/> + </outputs> + <tests> + <test> + <param name="bamInput" value="test1_sort.bam" dbkey="hg19" /> + <param name="vcfInput" value="test1.vcf" dbkey="hg19" /> + <param name="source" value="history" /> + <param name="exonAnno" value="exon_anno.RData" /> + <param name="proteinSeq" value="proseq.RData" /> + <param name="proCodingSeq" value="procodingseq.RData" /> + <param name="ids" value="ids.RData" /> + <output name="output_rpkm" file="test_rpkm.fasta" /> + <output name="output_snv" file="test_snv.fasta" /> + <output name="output_indel" file="test_indel.fasta" /> + </test> + </tests> + <help> +**Description** + +Generate protein FASTAs from exosome or transcriptome data (in the form of BAM files). </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btt543</citation> + <citation type="bibtex">@misc{toolsGalaxyP, author = {Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub +repository}, + year = {2017}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = +{$sha1$}" --> + </citations> +</tool>
--- a/test-data/test1.vcf Wed Jun 08 15:02:58 2016 -0400 +++ b/test-data/test1.vcf Fri Jan 13 12:18:32 2017 -0500 @@ -1,87 +1,87 @@ -##fileformat=VCFv4.1 -##samtoolsVersion=0.1.17 (r973:277) -##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth"> -##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"> -##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads"> -##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same"> -##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)"> -##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)"> -##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies"> -##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3"> -##INFO=<ID=CLR,Number=1,Type=Integer,Description="Log ratio of genotype likelihoods with and without the constraint"> -##INFO=<ID=UGT,Number=1,Type=String,Description="The most probable unconstrained genotype configuration in the trio"> -##INFO=<ID=CGT,Number=1,Type=String,Description="The most probable constrained genotype configuration in the trio"> -##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias"> -##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> -##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2."> -##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples."> -##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2."> -##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2."> -##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> -##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> -##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)"> -##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases"> -##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value"> -##FORMAT=<ID=PL,Number=-1,Type=Integer,Description="List of Phred-scaled genotype likelihoods, number of values is (#ALT+1)*(#ALT+2)/2"> -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT test -chr1 32386425 . T C 24 . DP=3;AF1=1;AC1=2;DP4=0,0,0,3;MQ=50;FQ=-36 GT:PL:GQ 1/1:56,9,0:15 -chr1 32507666 . G T 6.2 . DP=5;AF1=0.4999;AC1=1;DP4=3,0,2,0;MQ=50;FQ=8.65;PV4=1,0.062,1,0.36 GT:PL:GQ 0/1:35,0,78:36 -chr1 32524459 . A C 3.54 . DP=5;AF1=0.4998;AC1=1;DP4=1,2,0,2;MQ=50;FQ=5.47;PV4=1,0.0021,1,1 GT:PL:GQ 0/1:31,0,98:30 -chr1 32622505 . G A 101 . DP=18;AF1=0.5;AC1=1;DP4=10,0,5,2;MQ=50;FQ=104;PV4=0.15,0.0055,1,0.0075 GT:PL:GQ 0/1:131,0,162:99 -chr12 25357574 . CAA C 109 . INDEL;DP=5;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-46.5 GT:PL:GQ 1/1:149,12,0:21 -chr12 25357628 . TA T 53.4 . INDEL;DP=3;AF1=1;AC1=2;DP4=0,0,3,0;MQ=50;FQ=-43.5 GT:PL:GQ 1/1:93,9,0:16 -chr12 25358650 . A T 73 . DP=38;AF1=1;AC1=2;DP4=0,0,15,0;MQ=50;FQ=-72 GT:PL:GQ 1/1:106,45,0:87 -chr12 25358662 . CTTTTTTTT CTTTTTT,CTTTTTTT 31.6 . INDEL;DP=38;AF1=1;AC1=2;DP4=0,0,15,0;MQ=50;FQ=-52.5 GT:PL:GQ 1/1:96,42,24,91,0,64:33 -chr12 25358943 . T C 67.1 . DP=7;AF1=1;AC1=2;DP4=0,0,7,0;MQ=50;FQ=-48 GT:PL:GQ 1/1:100,21,0:39 -chr12 25358969 . T G 36.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:69,12,0:21 -chr12 25359352 . G A 172 . DP=16;AF1=1;AC1=2;DP4=0,0,14,0;MQ=50;FQ=-69 GT:PL:GQ 1/1:205,42,0:81 -chr12 25359464 . TAA TA 123 . INDEL;DP=26;AF1=1;AC1=2;DP4=0,0,26,0;MQ=50;FQ=-113 GT:PL:GQ 1/1:164,78,0:99 -chr12 25360138 . T C 169 . DP=21;AF1=1;AC1=2;DP4=0,0,19,0;MQ=50;FQ=-84 GT:PL:GQ 1/1:202,57,0:99 -chr12 25361091 . T C 93 . DP=15;AF1=1;AC1=2;DP4=0,0,14,0;MQ=50;FQ=-69 GT:PL:GQ 1/1:126,42,0:81 -chr12 25362217 . A G 179 . DP=20;AF1=1;AC1=2;DP4=0,0,20,0;MQ=50;FQ=-87 GT:PL:GQ 1/1:212,60,0:99 -chr12 25362465 . G A 38.3 . DP=18;AF1=1;AC1=2;DP4=0,0,5,0;MQ=50;FQ=-42 GT:PL:GQ 1/1:71,15,0:27 -chr12 25362552 . A C 156 . DP=10;AF1=1;AC1=2;DP4=0,0,10,0;MQ=50;FQ=-57 GT:PL:GQ 1/1:189,30,0:57 -chr12 25364387 . T C 21 . DP=7;AF1=0.5;AC1=1;DP4=3,1,0,2;MQ=50;FQ=24;PV4=0.4,1,1,1 GT:PL:GQ 0/1:51,0,112:54 -chr12 25368462 . C T 112 . DP=7;AF1=1;AC1=2;DP4=0,0,7,0;MQ=50;FQ=-48 GT:PL:GQ 1/1:145,21,0:39 -chr17 37866082 . G A 141 . DP=45;AF1=0.5;AC1=1;DP4=25,0,20,0;MQ=50;FQ=144;PV4=1,1,1,1 GT:PL:GQ 0/1:171,0,180:99 -chr17 37870047 . A G 30 . DP=3;AF1=0.5008;AC1=1;DP4=0,1,2,0;MQ=50;FQ=-4.12;PV4=0.33,1,1,1 GT:PL:GQ 0/1:60,0,25:28 -chr17 37879466 . G A 7.8 . DP=3;AF1=0.5001;AC1=1;DP4=1,0,1,1;MQ=50;FQ=4.79;PV4=1,0.064,1,1 GT:PL:GQ 0/1:37,0,31:34 -chr17 37885332 . G A 83.5 . DP=4;AF1=1;AC1=2;DP4=0,0,0,4;MQ=50;FQ=-39 GT:PL:GQ 1/1:116,12,0:21 -chr17 37898543 . T C 165 . DP=26;AF1=1;AC1=2;DP4=0,0,21,0;MQ=50;FQ=-90 GT:PL:GQ 1/1:198,63,0:99 -chr17 7530271 . C T 143 . DP=71;AF1=0.5;AC1=1;DP4=32,2,34,0;MQ=50;FQ=146;PV4=0.49,4.1e-06,1,1 GT:PL:GQ 0/1:173,0,238:99 -chr17 7572657 . G T 225 . DP=122;AF1=0.5;AC1=1;DP4=59,0,58,3;MQ=50;FQ=163;PV4=0.24,0.06,1,0.27 GT:PL:GQ 0/1:255,0,190:99 -chr17 7591866 . G T 45 . DP=14;AF1=0.5;AC1=1;DP4=10,0,4,0;MQ=50;FQ=48;PV4=1,0.062,1,0.01 GT:PL:GQ 0/1:75,0,162:78 -chr17 7606153 . C T 74 . DP=16;AF1=0.5;AC1=1;DP4=10,0,5,0;MQ=50;FQ=77;PV4=1,0.12,1,1 GT:PL:GQ 0/1:104,0,165:99 -chr2 48010558 . C A 12.3 . DP=7;AF1=0.5002;AC1=1;DP4=1,0,2,0;MQ=50;FQ=5.23;PV4=1,0.065,1,1 GT:PL:GQ 0/1:42,0,31:34 -chr2 48016554 . T C 32 . DP=4;AF1=0.5;AC1=1;DP4=1,1,2,0;MQ=50;FQ=20.9;PV4=1,1,1,0.21 GT:PL:GQ 0/1:62,0,48:51 -chr2 48018081 . A G 77 . DP=6;AF1=0.501;AC1=1;DP4=1,0,4,0;MQ=50;FQ=-4.75;PV4=1,1,1,0.34 GT:PL:GQ 0/1:107,0,24:27 -chr2 48018221 . C T 22 . DP=7;AF1=0.5;AC1=1;DP4=5,0,2,0;MQ=50;FQ=25;PV4=1,1,1,1 GT:PL:GQ 0/1:52,0,116:55 -chr2 48027990 . G T 122 . DP=17;AF1=0.5;AC1=1;DP4=7,0,9,0;MQ=50;FQ=104;PV4=1,1,1,0.039 GT:PL:GQ 0/1:152,0,131:99 -chr2 48030458 . G C 105 . DP=4;AF1=1;AC1=2;DP4=0,0,3,1;MQ=50;FQ=-39 GT:PL:GQ 1/1:137,12,0:21 -chr5 112154737 . CT C 29 . INDEL;DP=5;AF1=0.5;AC1=1;DP4=3,0,2,0;MQ=50;FQ=32;PV4=1,1,1,0.0012 GT:PL:GQ 0/1:59,0,85:62 -chr5 112162854 . T C 60 . DP=3;AF1=1;AC1=2;DP4=0,0,3,0;MQ=50;FQ=-36 GT:PL:GQ 1/1:92,9,0:16 -chr5 112164561 . G A 87.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:120,12,0:21 -chr5 112175639 . C T 31 . DP=4;AF1=0.5;AC1=1;DP4=2,0,2,0;MQ=50;FQ=31.5;PV4=1,0.21,1,1 GT:PL:GQ 0/1:61,0,62:61 -chr5 112175897 . GAA GA 7.8 . INDEL;DP=7;AF1=0.5;AC1=1;DP4=4,0,3,0;MQ=50;FQ=10.4;PV4=1,0.0018,1,0.33 GT:PL:GQ 0/1:37,0,97:39 -chr5 112176559 . T G 72 . DP=11;AF1=1;AC1=2;DP4=0,0,8,0;MQ=50;FQ=-51 GT:PL:GQ 1/1:105,24,0:45 -chr5 112176756 . T A 143 . DP=10;AF1=1;AC1=2;DP4=0,0,9,0;MQ=50;FQ=-54 GT:PL:GQ 1/1:176,27,0:51 -chr5 112180015 . C A 123 . DP=11;AF1=0.5;AC1=1;DP4=3,0,8,0;MQ=50;FQ=40;PV4=1,1,1,1 GT:PL:GQ 0/1:153,0,67:70 -chr5 112204170 . G A 112 . DP=5;AF1=1;AC1=2;DP4=0,0,2,2;MQ=50;FQ=-39 GT:PL:GQ 1/1:144,12,0:21 -chr7 140043303 . C T 88 . DP=18;AF1=0.5;AC1=1;DP4=11,0,7,0;MQ=50;FQ=91;PV4=1,0.00034,1,0.42 GT:PL:GQ 0/1:118,0,167:99 -chr7 140065806 . T C 38.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:71,12,0:21 -chr7 140065845 . C A 44.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:77,12,0:21 -chr7 140152904 . CAAAA CAAAAA 41.5 . INDEL;DP=42;AF1=0.5;AC1=1;DP4=23,0,16,0;MQ=50;FQ=44.2;PV4=1,1,1,1 GT:PL:GQ 0/1:79,0,91:82 -chr7 140153495 . G T 140 . DP=52;AF1=0.5;AC1=1;DP4=28,0,22,0;MQ=50;FQ=143;PV4=1,0.082,1,0.00038 GT:PL:GQ 0/1:170,0,184:99 -chr7 140158851 . C G 153 . DP=36;AF1=1;AC1=2;DP4=1,0,33,0;MQ=50;FQ=-102;PV4=1,1,1,1 GT:PL:GQ 1/1:186,75,0:99 -chr7 140244560 . C T 78 . DP=6;AF1=0.5013;AC1=1;DP4=1,0,4,0;MQ=50;FQ=-5.45;PV4=1,1,1,1 GT:PL:GQ 0/1:108,0,23:26 -chr7 140406430 . T A 8.64 . DP=27;AF1=0.5;AC1=1;DP4=19,0,6,0;MQ=50;FQ=11.3;PV4=1,1,1,0.00021 GT:PL:GQ 0/1:38,0,167:40 -chr7 140406436 . A G 4.77 . DP=14;AF1=0.4999;AC1=1;DP4=12,0,2,0;MQ=50;FQ=6.99;PV4=1,1,1,0.08 GT:PL:GQ 0/1:33,0,170:33 -chr7 140424582 . G C 18.1 . DP=5;AF1=0.5;AC1=1;DP4=0,2,1,2;MQ=50;FQ=20.4;PV4=1,0.00086,1,1 GT:PL:GQ 0/1:48,0,56:50 -chr7 140426098 . G A 10.2 . DP=3;AF1=1;AC1=2;DP4=0,0,2,0;MQ=50;FQ=-33 GT:PL:GQ 1/1:41,6,0:8 -chr7 140702871 . G A 77.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:110,12,0:21 -chr7 140706061 . G T 119 . DP=74;AF1=0.5;AC1=1;DP4=45,0,22,0;MQ=50;FQ=122;PV4=1,1,1,1 GT:PL:GQ 0/1:149,0,178:99 -chr7 140706157 . G T 42 . DP=25;AF1=0.5;AC1=1;DP4=13,0,9,0;MQ=50;FQ=45;PV4=1,5.7e-11,1,0.013 GT:PL:GQ 0/1:72,0,170:75 -chr9 86583076 . C T 64 . DP=17;AF1=0.5;AC1=1;DP4=5,0,11,0;MQ=50;FQ=66;PV4=1,1.4e-08,1,1 GT:PL:GQ 0/1:94,0,100:96 -chr9 86593314 . G C 186 . DP=203;AF1=0.5;AC1=1;DP4=100,0,99,0;MQ=50;FQ=186;PV4=1,1,1,0.072 GT:PL:GQ 0/1:216,0,216:99 -chr9 86595070 . C T 140 . DP=93;AF1=0.5;AC1=1;DP4=53,0,38,0;MQ=50;FQ=143;PV4=1,0.43,1,1 GT:PL:GQ 0/1:170,0,188:99 -chr9 86595498 . G A 66 . DP=128;AF1=0.5;AC1=1;DP4=50,2,76,0;MQ=50;FQ=69;PV4=0.16,6e-81,1,1 GT:PL:GQ 0/1:96,0,225:99 +##fileformat=VCFv4.1 +##samtoolsVersion=0.1.17 (r973:277) +##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth"> +##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"> +##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads"> +##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same"> +##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)"> +##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)"> +##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies"> +##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3"> +##INFO=<ID=CLR,Number=1,Type=Integer,Description="Log ratio of genotype likelihoods with and without the constraint"> +##INFO=<ID=UGT,Number=1,Type=String,Description="The most probable unconstrained genotype configuration in the trio"> +##INFO=<ID=CGT,Number=1,Type=String,Description="The most probable constrained genotype configuration in the trio"> +##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias"> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> +##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2."> +##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples."> +##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2."> +##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2."> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases"> +##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value"> +##FORMAT=<ID=PL,Number=-1,Type=Integer,Description="List of Phred-scaled genotype likelihoods, number of values is (#ALT+1)*(#ALT+2)/2"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT test +chr1 32386425 . T C 24 . DP=3;AF1=1;AC1=2;DP4=0,0,0,3;MQ=50;FQ=-36 GT:PL:GQ 1/1:56,9,0:15 +chr1 32507666 . G T 6.2 . DP=5;AF1=0.4999;AC1=1;DP4=3,0,2,0;MQ=50;FQ=8.65;PV4=1,0.062,1,0.36 GT:PL:GQ 0/1:35,0,78:36 +chr1 32524459 . A C 3.54 . DP=5;AF1=0.4998;AC1=1;DP4=1,2,0,2;MQ=50;FQ=5.47;PV4=1,0.0021,1,1 GT:PL:GQ 0/1:31,0,98:30 +chr1 32622505 . G A 101 . DP=18;AF1=0.5;AC1=1;DP4=10,0,5,2;MQ=50;FQ=104;PV4=0.15,0.0055,1,0.0075 GT:PL:GQ 0/1:131,0,162:99 +chr12 25357574 . CAA C 109 . INDEL;DP=5;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-46.5 GT:PL:GQ 1/1:149,12,0:21 +chr12 25357628 . TA T 53.4 . INDEL;DP=3;AF1=1;AC1=2;DP4=0,0,3,0;MQ=50;FQ=-43.5 GT:PL:GQ 1/1:93,9,0:16 +chr12 25358650 . A T 73 . DP=38;AF1=1;AC1=2;DP4=0,0,15,0;MQ=50;FQ=-72 GT:PL:GQ 1/1:106,45,0:87 +chr12 25358662 . CTTTTTTTT CTTTTTT,CTTTTTTT 31.6 . INDEL;DP=38;AF1=1;AC1=2;DP4=0,0,15,0;MQ=50;FQ=-52.5 GT:PL:GQ 1/1:96,42,24,91,0,64:33 +chr12 25358943 . T C 67.1 . DP=7;AF1=1;AC1=2;DP4=0,0,7,0;MQ=50;FQ=-48 GT:PL:GQ 1/1:100,21,0:39 +chr12 25358969 . T G 36.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:69,12,0:21 +chr12 25359352 . G A 172 . DP=16;AF1=1;AC1=2;DP4=0,0,14,0;MQ=50;FQ=-69 GT:PL:GQ 1/1:205,42,0:81 +chr12 25359464 . TAA TA 123 . INDEL;DP=26;AF1=1;AC1=2;DP4=0,0,26,0;MQ=50;FQ=-113 GT:PL:GQ 1/1:164,78,0:99 +chr12 25360138 . T C 169 . DP=21;AF1=1;AC1=2;DP4=0,0,19,0;MQ=50;FQ=-84 GT:PL:GQ 1/1:202,57,0:99 +chr12 25361091 . T C 93 . DP=15;AF1=1;AC1=2;DP4=0,0,14,0;MQ=50;FQ=-69 GT:PL:GQ 1/1:126,42,0:81 +chr12 25362217 . A G 179 . DP=20;AF1=1;AC1=2;DP4=0,0,20,0;MQ=50;FQ=-87 GT:PL:GQ 1/1:212,60,0:99 +chr12 25362465 . G A 38.3 . DP=18;AF1=1;AC1=2;DP4=0,0,5,0;MQ=50;FQ=-42 GT:PL:GQ 1/1:71,15,0:27 +chr12 25362552 . A C 156 . DP=10;AF1=1;AC1=2;DP4=0,0,10,0;MQ=50;FQ=-57 GT:PL:GQ 1/1:189,30,0:57 +chr12 25364387 . T C 21 . DP=7;AF1=0.5;AC1=1;DP4=3,1,0,2;MQ=50;FQ=24;PV4=0.4,1,1,1 GT:PL:GQ 0/1:51,0,112:54 +chr12 25368462 . C T 112 . DP=7;AF1=1;AC1=2;DP4=0,0,7,0;MQ=50;FQ=-48 GT:PL:GQ 1/1:145,21,0:39 +chr17 37866082 . G A 141 . DP=45;AF1=0.5;AC1=1;DP4=25,0,20,0;MQ=50;FQ=144;PV4=1,1,1,1 GT:PL:GQ 0/1:171,0,180:99 +chr17 37870047 . A G 30 . DP=3;AF1=0.5008;AC1=1;DP4=0,1,2,0;MQ=50;FQ=-4.12;PV4=0.33,1,1,1 GT:PL:GQ 0/1:60,0,25:28 +chr17 37879466 . G A 7.8 . DP=3;AF1=0.5001;AC1=1;DP4=1,0,1,1;MQ=50;FQ=4.79;PV4=1,0.064,1,1 GT:PL:GQ 0/1:37,0,31:34 +chr17 37885332 . G A 83.5 . DP=4;AF1=1;AC1=2;DP4=0,0,0,4;MQ=50;FQ=-39 GT:PL:GQ 1/1:116,12,0:21 +chr17 37898543 . T C 165 . DP=26;AF1=1;AC1=2;DP4=0,0,21,0;MQ=50;FQ=-90 GT:PL:GQ 1/1:198,63,0:99 +chr17 7530271 . C T 143 . DP=71;AF1=0.5;AC1=1;DP4=32,2,34,0;MQ=50;FQ=146;PV4=0.49,4.1e-06,1,1 GT:PL:GQ 0/1:173,0,238:99 +chr17 7572657 . G T 225 . DP=122;AF1=0.5;AC1=1;DP4=59,0,58,3;MQ=50;FQ=163;PV4=0.24,0.06,1,0.27 GT:PL:GQ 0/1:255,0,190:99 +chr17 7591866 . G T 45 . DP=14;AF1=0.5;AC1=1;DP4=10,0,4,0;MQ=50;FQ=48;PV4=1,0.062,1,0.01 GT:PL:GQ 0/1:75,0,162:78 +chr17 7606153 . C T 74 . DP=16;AF1=0.5;AC1=1;DP4=10,0,5,0;MQ=50;FQ=77;PV4=1,0.12,1,1 GT:PL:GQ 0/1:104,0,165:99 +chr2 48010558 . C A 12.3 . DP=7;AF1=0.5002;AC1=1;DP4=1,0,2,0;MQ=50;FQ=5.23;PV4=1,0.065,1,1 GT:PL:GQ 0/1:42,0,31:34 +chr2 48016554 . T C 32 . DP=4;AF1=0.5;AC1=1;DP4=1,1,2,0;MQ=50;FQ=20.9;PV4=1,1,1,0.21 GT:PL:GQ 0/1:62,0,48:51 +chr2 48018081 . A G 77 . DP=6;AF1=0.501;AC1=1;DP4=1,0,4,0;MQ=50;FQ=-4.75;PV4=1,1,1,0.34 GT:PL:GQ 0/1:107,0,24:27 +chr2 48018221 . C T 22 . DP=7;AF1=0.5;AC1=1;DP4=5,0,2,0;MQ=50;FQ=25;PV4=1,1,1,1 GT:PL:GQ 0/1:52,0,116:55 +chr2 48027990 . G T 122 . DP=17;AF1=0.5;AC1=1;DP4=7,0,9,0;MQ=50;FQ=104;PV4=1,1,1,0.039 GT:PL:GQ 0/1:152,0,131:99 +chr2 48030458 . G C 105 . DP=4;AF1=1;AC1=2;DP4=0,0,3,1;MQ=50;FQ=-39 GT:PL:GQ 1/1:137,12,0:21 +chr5 112154737 . CT C 29 . INDEL;DP=5;AF1=0.5;AC1=1;DP4=3,0,2,0;MQ=50;FQ=32;PV4=1,1,1,0.0012 GT:PL:GQ 0/1:59,0,85:62 +chr5 112162854 . T C 60 . DP=3;AF1=1;AC1=2;DP4=0,0,3,0;MQ=50;FQ=-36 GT:PL:GQ 1/1:92,9,0:16 +chr5 112164561 . G A 87.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:120,12,0:21 +chr5 112175639 . C T 31 . DP=4;AF1=0.5;AC1=1;DP4=2,0,2,0;MQ=50;FQ=31.5;PV4=1,0.21,1,1 GT:PL:GQ 0/1:61,0,62:61 +chr5 112175897 . GAA GA 7.8 . INDEL;DP=7;AF1=0.5;AC1=1;DP4=4,0,3,0;MQ=50;FQ=10.4;PV4=1,0.0018,1,0.33 GT:PL:GQ 0/1:37,0,97:39 +chr5 112176559 . T G 72 . DP=11;AF1=1;AC1=2;DP4=0,0,8,0;MQ=50;FQ=-51 GT:PL:GQ 1/1:105,24,0:45 +chr5 112176756 . T A 143 . DP=10;AF1=1;AC1=2;DP4=0,0,9,0;MQ=50;FQ=-54 GT:PL:GQ 1/1:176,27,0:51 +chr5 112180015 . C A 123 . DP=11;AF1=0.5;AC1=1;DP4=3,0,8,0;MQ=50;FQ=40;PV4=1,1,1,1 GT:PL:GQ 0/1:153,0,67:70 +chr5 112204170 . G A 112 . DP=5;AF1=1;AC1=2;DP4=0,0,2,2;MQ=50;FQ=-39 GT:PL:GQ 1/1:144,12,0:21 +chr7 140043303 . C T 88 . DP=18;AF1=0.5;AC1=1;DP4=11,0,7,0;MQ=50;FQ=91;PV4=1,0.00034,1,0.42 GT:PL:GQ 0/1:118,0,167:99 +chr7 140065806 . T C 38.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:71,12,0:21 +chr7 140065845 . C A 44.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:77,12,0:21 +chr7 140152904 . CAAAA CAAAAA 41.5 . INDEL;DP=42;AF1=0.5;AC1=1;DP4=23,0,16,0;MQ=50;FQ=44.2;PV4=1,1,1,1 GT:PL:GQ 0/1:79,0,91:82 +chr7 140153495 . G T 140 . DP=52;AF1=0.5;AC1=1;DP4=28,0,22,0;MQ=50;FQ=143;PV4=1,0.082,1,0.00038 GT:PL:GQ 0/1:170,0,184:99 +chr7 140158851 . C G 153 . DP=36;AF1=1;AC1=2;DP4=1,0,33,0;MQ=50;FQ=-102;PV4=1,1,1,1 GT:PL:GQ 1/1:186,75,0:99 +chr7 140244560 . C T 78 . DP=6;AF1=0.5013;AC1=1;DP4=1,0,4,0;MQ=50;FQ=-5.45;PV4=1,1,1,1 GT:PL:GQ 0/1:108,0,23:26 +chr7 140406430 . T A 8.64 . DP=27;AF1=0.5;AC1=1;DP4=19,0,6,0;MQ=50;FQ=11.3;PV4=1,1,1,0.00021 GT:PL:GQ 0/1:38,0,167:40 +chr7 140406436 . A G 4.77 . DP=14;AF1=0.4999;AC1=1;DP4=12,0,2,0;MQ=50;FQ=6.99;PV4=1,1,1,0.08 GT:PL:GQ 0/1:33,0,170:33 +chr7 140424582 . G C 18.1 . DP=5;AF1=0.5;AC1=1;DP4=0,2,1,2;MQ=50;FQ=20.4;PV4=1,0.00086,1,1 GT:PL:GQ 0/1:48,0,56:50 +chr7 140426098 . G A 10.2 . DP=3;AF1=1;AC1=2;DP4=0,0,2,0;MQ=50;FQ=-33 GT:PL:GQ 1/1:41,6,0:8 +chr7 140702871 . G A 77.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:110,12,0:21 +chr7 140706061 . G T 119 . DP=74;AF1=0.5;AC1=1;DP4=45,0,22,0;MQ=50;FQ=122;PV4=1,1,1,1 GT:PL:GQ 0/1:149,0,178:99 +chr7 140706157 . G T 42 . DP=25;AF1=0.5;AC1=1;DP4=13,0,9,0;MQ=50;FQ=45;PV4=1,5.7e-11,1,0.013 GT:PL:GQ 0/1:72,0,170:75 +chr9 86583076 . C T 64 . DP=17;AF1=0.5;AC1=1;DP4=5,0,11,0;MQ=50;FQ=66;PV4=1,1.4e-08,1,1 GT:PL:GQ 0/1:94,0,100:96 +chr9 86593314 . G C 186 . DP=203;AF1=0.5;AC1=1;DP4=100,0,99,0;MQ=50;FQ=186;PV4=1,1,1,0.072 GT:PL:GQ 0/1:216,0,216:99 +chr9 86595070 . C T 140 . DP=93;AF1=0.5;AC1=1;DP4=53,0,38,0;MQ=50;FQ=143;PV4=1,0.43,1,1 GT:PL:GQ 0/1:170,0,188:99 +chr9 86595498 . G A 66 . DP=128;AF1=0.5;AC1=1;DP4=50,2,76,0;MQ=50;FQ=69;PV4=0.16,6e-81,1,1 GT:PL:GQ 0/1:96,0,225:99
--- a/tool_data_table_conf.xml.sample Wed Jun 08 15:02:58 2016 -0400 +++ b/tool_data_table_conf.xml.sample Fri Jan 13 12:18:32 2017 -0500 @@ -1,7 +1,7 @@ -<tables> - <!-- Locations of all customProDB annotations under genome directory --> - <table name="customProDB" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/customProDB.loc" /> - </table> -</tables> +<tables> + <!-- Locations of all customProDB annotations under genome directory --> + <table name="customProDB" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/customProDB.loc" /> + </table> +</tables>