Mercurial > repos > iuc > snpsift_dbnsfp
view test-data/test_dbnsfp_out.vcf @ 2:c838e7136a40 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
| author | iuc |
|---|---|
| date | Mon, 05 Dec 2016 12:06:13 -0500 |
| parents | dc480609d9c1 |
| children |
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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 ] )' "> ##SnpSiftVersion="SnpSift 3.5 (build 2014-02-12), by Pablo Cingolani" ##SnpSiftCmd="SnpSift dbnsfp /Users/jj/gxt/gxt/database/files/005/dataset_5011_files/dbNSFP.gz -f aaref,aaalt,genename,aapos,SIFT_score /Users/jj/gxt/gxt/database/files/005/dataset_5006.dat " ##INFO=<ID=dbNSFP_aapos,Number=A,Type=Integer,Description="Field 'aapos' from dbNSFP"> ##INFO=<ID=dbNSFP_genename,Number=A,Type=String,Description="Field 'genename' from dbNSFP"> ##INFO=<ID=dbNSFP_aaref,Number=A,Type=Character,Description="Field 'aaref' from dbNSFP"> ##INFO=<ID=dbNSFP_aaalt,Number=A,Type=Character,Description="Field 'aaalt' from dbNSFP"> ##INFO=<ID=dbNSFP_SIFT_score,Number=A,Type=Float,Description="Field 'SIFT_score' from dbNSFP"> #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);dbNSFP_aapos=48|8|48;dbNSFP_genename=ADH1B;dbNSFP_aaref=H;dbNSFP_aaalt=R;dbNSFP_SIFT_score=0.15