Mercurial > repos > jjohnson > snpsift
comparison test-data/test_rmInfo.vcf @ 2:49b5bd3dc316
Add rmInfo tool
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Tue, 21 Oct 2014 12:17:25 -0500 |
| parents | |
| children | 1739678def32 |
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| 1:796388c291d3 | 2:49b5bd3dc316 |
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| 1 ##fileformat=VCFv4.1 | |
| 2 ##samtoolsVersion=0.1.18 (r982:295) | |
| 3 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth"> | |
| 4 ##SnpEffVersion="3.5 (build 2014-02-12), by Pablo Cingolani" | |
| 5 ##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 " | |
| 6 ##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 ] )' "> | |
| 7 #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 | |
| 8 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) | |
| 9 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) | |
| 10 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) |