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view test-data/test_rmInfo.vcf @ 2:49b5bd3dc316

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Add rmInfo tool
author Jim Johnson <jj@umn.edu>
date Tue, 21 Oct 2014 12:17:25 -0500
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children 1739678def32
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##fileformat=VCFv4.1
##samtoolsVersion=0.1.18 (r982:295)
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
##SnpEffVersion="3.5 (build 2014-02-12), by Pablo Cingolani"
##SnpEffCmd="SnpEff  -i vcf -o vcf -upDownStreamLen 5000 -spliceSiteSize 1 -stats /Users/jj/gxt/gxt/database/files/004/dataset_4998.dat GRCh37.71 /Users/jj/gxt/gxt/database/files/004/dataset_4996.dat "
##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank  | Genotype_Number [ | ERRORS | WARNINGS ] )' ">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	/data/sequencing/output/biotec4/mapping/L774.q1.s.bam	/data/sequencing/output/biotec4/mapping/L775.q1.s.bam
chr4	100239319	rs1229984	T	C	94.3	.	DP=29;EFF=EXON(MODIFIER|||||ADH1B|processed_transcript|CODING|ENST00000504498|3|1),EXON(MODIFIER|||||ADH1B|retained_intron|CODING|ENST00000515694|3|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H48R|375|ADH1B|protein_coding|CODING|ENST00000305046|3|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H8R|335|ADH1B|protein_coding|CODING|ENST00000394887|3|1),UTR_3_PRIME(MODIFIER||2729|||ADH1B|nonsense_mediated_decay|CODING|ENST00000506651|4|1)
chr12	32491626	rs1471909	G	A	124.0	.	DP=22;EFF=DOWNSTREAM(MODIFIER||532|||BICD1|retained_intron|CODING|ENST00000552160||1),INTRON(MODIFIER||||835|BICD1|protein_coding|CODING|ENST00000548411|7|1),INTRON(MODIFIER||||975|BICD1|protein_coding|CODING|ENST00000281474|7|1),INTRON(MODIFIER|||||BICD1|nonsense_mediated_decay|CODING|ENST00000395758|7|1),INTRON(MODIFIER|||||BICD1|retained_intron|CODING|ENST00000552226|1|1)
chrX	153010066	rs11803	C	T	73.8	.	DP=34;EFF=DOWNSTREAM(MODIFIER||4008||221|ABCD1|protein_coding|CODING|ENST00000443684||1),INTRAGENIC(MODIFIER|||||ABCD1||CODING|||1),INTRON(MODIFIER|||||U52111.14|antisense|NON_CODING|ENST00000434284|1|1),UTR_3_PRIME(MODIFIER||877||745|ABCD1|protein_coding|CODING|ENST00000218104|10|1)