snpsift: test-data/test_rmInfo.vcf annotate

annotate test-data/test_rmInfo.vcf @ 8:2f40467536cf draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 93465571cf180554c3548338a68fa0f1604985dc-dirty

author	jjohnson
date	Sat, 09 Apr 2016 11:53:30 -0400
parents	1739678def32
children

rev	line source
2 49b5bd3dc316 Add rmInfo tool Jim Johnson <jj@umn.edu> parents: diff changeset	1 ##fileformat=VCFv4.1
49b5bd3dc316 Add rmInfo tool Jim Johnson <jj@umn.edu> parents: diff changeset	2 ##samtoolsVersion=0.1.18 (r982:295)
49b5bd3dc316 Add rmInfo tool Jim Johnson <jj@umn.edu> parents: diff changeset	3 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
49b5bd3dc316 Add rmInfo tool Jim Johnson <jj@umn.edu> parents: diff changeset	4 ##SnpEffVersion="3.5 (build 2014-02-12), by Pablo Cingolani"
49b5bd3dc316 Add rmInfo tool Jim Johnson <jj@umn.edu> 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 "
49b5bd3dc316 Add rmInfo tool Jim Johnson <jj@umn.edu> 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 ] )' ">
3 1739678def32 Add vcfCheck and test cases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	7 #CHROM POS ID REF ALT QUAL FILTER INFO
2 49b5bd3dc316 Add rmInfo tool Jim Johnson <jj@umn.edu> parents: diff changeset	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)
49b5bd3dc316 Add rmInfo tool Jim Johnson <jj@umn.edu> parents: diff changeset	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)
49b5bd3dc316 Add rmInfo tool Jim Johnson <jj@umn.edu> parents: diff changeset	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)