Mercurial > repos > jjohnson > snpeff_to_peptides
comparison test-data/snpeff.vcf @ 0:41a666a3d8a5 draft default tip
Uploaded
| author | jjohnson |
|---|---|
| date | Tue, 17 Dec 2013 18:45:13 -0500 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:41a666a3d8a5 |
|---|---|
| 1 ##fileformat=VCFv4.1 | |
| 2 ##samtoolsVersion=0.1.18 (r982:295) | |
| 3 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth"> | |
| 4 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"> | |
| 5 ##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads"> | |
| 6 ##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same"> | |
| 7 ##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)"> | |
| 8 ##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)"> | |
| 9 ##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies"> | |
| 10 ##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3"> | |
| 11 ##INFO=<ID=CLR,Number=1,Type=Integer,Description="Log ratio of genotype likelihoods with and without the constraint"> | |
| 12 ##INFO=<ID=UGT,Number=1,Type=String,Description="The most probable unconstrained genotype configuration in the trio"> | |
| 13 ##INFO=<ID=CGT,Number=1,Type=String,Description="The most probable constrained genotype configuration in the trio"> | |
| 14 ##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias"> | |
| 15 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> | |
| 16 ##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2."> | |
| 17 ##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples."> | |
| 18 ##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2."> | |
| 19 ##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2."> | |
| 20 ##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias"> | |
| 21 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | |
| 22 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> | |
| 23 ##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)"> | |
| 24 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases"> | |
| 25 ##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value"> | |
| 26 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods"> | |
| 27 ##SnpEffVersion="3.4 (build 2013-11-27), by Pablo Cingolani" | |
| 28 ##SnpEffCmd="SnpEff -i vcf -o vcf -upDownStreamLen 5000 -spliceSiteSize 1 -snp -no-downstream -no-intergenic -no-intron -no-upstream -no-utr -stats /galaxy/PRODUCTION/database/files/000/376/dataset_376197.dat GRCh37.73 /galaxy/PRODUCTION/database/files/000/376/dataset_376194.dat " | |
| 29 ##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 ] )' "> | |
| 30 ##SnpEffCmd="SnpEff -i vcf -o vcf -upDownStreamLen 5000 -spliceSiteSize 1 -geneId -no-downstream -no-intergenic -no-intron -no-upstream -no-utr -stats /galaxy/PRODUCTION/database/files/000/376/dataset_376199.dat GRCh37.73 /galaxy/PRODUCTION/database/files/000/376/dataset_376196.dat " | |
| 31 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT /galaxy/PRODUCTION/database/tmp/tmp-SAMTOOLS-BmXdVn/bam_input_0.bam | |
| 32 chr1 22846709 . G A 9.31 . DP=2;VDB=0.0174;AF1=1;AC1=2;DP4=0,0,1,1;MQ=20;FQ=-33;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V885M|1127|ZBTB40|protein_coding|CODING|ENST00000374651|12|1) PL 40,6,0 | |
| 33 chr1 36752433 . C T 6.02 . DP=2;VDB=0.0099;AF1=1;AC1=2;DP4=0,0,2,0;MQ=20;FQ=-33;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A201V|955|THRAP3|protein_coding|CODING|ENST00000354618|4|1) PL 36,6,0 | |
| 34 chr1 89449390 . T C 15.1 . DP=3;VDB=0.0214;AF1=1;AC1=2;DP4=0,0,1,2;MQ=20;FQ=-36;EFF=EXON(MODIFIER|||||RBMXL1|processed_transcript|CODING|ENST00000413769|3|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atA/atG|I40M|390|RBMXL1|protein_coding|CODING|ENST00000321792|2|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atA/atG|I40M|390|RBMXL1|protein_coding|CODING|ENST00000399794|3|1);EFF=EXON(MODIFIER|||||ENSG00000213516|processed_transcript|CODING|ENST00000413769|3|1) PL 47,9,0 | |
| 35 chr1 89449434 . T C 9.31 . DP=2;VDB=0.0120;AF1=1;AC1=2;DP4=0,0,1,1;MQ=20;FQ=-33;EFF=EXON(MODIFIER|||||RBMXL1|processed_transcript|CODING|ENST00000413769|3|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T26A|390|RBMXL1|protein_coding|CODING|ENST00000321792|2|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T26A|390|RBMXL1|protein_coding|CODING|ENST00000399794|3|1);EFF=EXON(MODIFIER|||||ENSG00000213516|processed_transcript|CODING|ENST00000413769|3|1) PL 40,6,0 |