snpsift_dbnsfp_generic: test-data/test_dbnsfp_out.vcf annotate

annotate test-data/test_dbnsfp_out.vcf @ 1:1f4ee04c0841 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp_generic/ commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f

author	iuc
date	Mon, 05 Dec 2016 12:06:09 -0500
parents	0624d484adba
children

rev	line source
0 0624d484adba Uploaded iuc parents: diff changeset	1 ##fileformat=VCFv4.1
0624d484adba Uploaded iuc parents: diff changeset	2 ##samtoolsVersion=0.1.18 (r982:295)
0624d484adba Uploaded iuc parents: diff changeset	3 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
0624d484adba Uploaded iuc parents: diff changeset	4 ##SnpEffVersion="3.5 (build 2014-02-12), by Pablo Cingolani"
0624d484adba Uploaded iuc parents: diff changeset	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 "
0624d484adba Uploaded iuc parents: diff changeset	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 ] )' ">
0624d484adba Uploaded iuc parents: diff changeset	7 ##SnpSiftVersion="SnpSift 3.5 (build 2014-02-12), by Pablo Cingolani"
0624d484adba Uploaded iuc parents: diff changeset	8 ##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 "
0624d484adba Uploaded iuc parents: diff changeset	9 ##INFO=<ID=dbNSFP_aapos,Number=A,Type=Integer,Description="Field 'aapos' from dbNSFP">
0624d484adba Uploaded iuc parents: diff changeset	10 ##INFO=<ID=dbNSFP_genename,Number=A,Type=String,Description="Field 'genename' from dbNSFP">
0624d484adba Uploaded iuc parents: diff changeset	11 ##INFO=<ID=dbNSFP_aaref,Number=A,Type=Character,Description="Field 'aaref' from dbNSFP">
0624d484adba Uploaded iuc parents: diff changeset	12 ##INFO=<ID=dbNSFP_aaalt,Number=A,Type=Character,Description="Field 'aaalt' from dbNSFP">
0624d484adba Uploaded iuc parents: diff changeset	13 ##INFO=<ID=dbNSFP_SIFT_score,Number=A,Type=Float,Description="Field 'SIFT_score' from dbNSFP">
0624d484adba Uploaded iuc parents: diff changeset	14 #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
0624d484adba Uploaded iuc parents: diff changeset	15 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