snpeff_cds_report: test-data/snpeff.vcf annotate

annotate test-data/snpeff.vcf @ 4:429a6b4df5e5

Restrict to info items that are key=value pairs

author	Jim Johnson <jj@umn.edu>
date	Wed, 24 Apr 2013 08:00:04 -0500
parents	cdbdac66d6b5
children

rev	line source
0 cdbdac66d6b5 Uploaded jjohnson parents: diff changeset	1 ##SnpEffVersion="SnpEff 3.1k (build 2012-12-17), by Pablo Cingolani"
cdbdac66d6b5 Uploaded jjohnson parents: diff changeset	2 ##SnpEffCmd="SnpEff -i vcf -o vcf -upDownStreamLen 0 -no downstream,intergenic,intron,upstream,utr -stats /galaxy/PRODUCTION/database/files/000/246/dataset_246290.dat GRCh37.66 /galaxy/PRODUCTION/database/files/000/246/dataset_246288.dat "
cdbdac66d6b5 Uploaded jjohnson parents: diff changeset	3 ##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 \| Gene_BioType \| Coding \| Transcript \| Exon [ \| ERRORS \| WARNINGS ] )' ">
cdbdac66d6b5 Uploaded jjohnson parents: diff changeset	4 chr1 46871931 . GC G . PASS SAF=0.333333;DP=6;EFF=EXON(MODIFIER\|\|\|\|\|FAAH\|processed_transcript\|CODING\|ENST00000489366\|2),EXON(MODIFIER\|\|\|\|\|FAAH\|processed_transcript\|CODING\|ENST00000493735\|6),FRAME_SHIFT(HIGH\|\|-\|-281\|579\|FAAH\|protein_coding\|CODING\|ENST00000243167\|7)
cdbdac66d6b5 Uploaded jjohnson parents: diff changeset	5 chr1 54291558 . G GA . PASS SAF=0.333333;DP=12;EFF=EXON(MODIFIER\|\|\|\|\|TMEM48\|processed_transcript\|CODING\|ENST00000480952\|4),FRAME_SHIFT(HIGH\|\|-/T\|-169?\|542\|TMEM48\|protein_coding\|CODING\|ENST00000540001\|5),FRAME_SHIFT(HIGH\|\|-/T\|-169?\|557\|TMEM48\|protein_coding\|CODING\|ENST00000360494\|5),FRAME_SHIFT(HIGH\|\|-/T\|-169?\|674\|TMEM48\|protein_coding\|CODING\|ENST00000371429\|5),FRAME_SHIFT(HIGH\|\|-/T\|-54?\|559\|TMEM48\|protein_coding\|CODING\|ENST00000234725\|4)
cdbdac66d6b5 Uploaded jjohnson parents: diff changeset	6 chr1 109461327 . G A,GA . PASS SAF=0.333333,SAF=0.333333;DP=6;EFF=FRAME_SHIFT(HIGH\|\|-/A\|-453?\|684\|GPSM2\|protein_coding\|CODING\|ENST00000264126\|12),FRAME_SHIFT(HIGH\|\|-/A\|-453?\|684\|GPSM2\|protein_coding\|CODING\|ENST00000406462\|13),SYNONYMOUS_CODING(LOW\|SILENT\|ggG/ggA\|G452\|684\|GPSM2\|protein_coding\|CODING\|ENST00000264126\|),SYNONYMOUS_CODING(LOW\|SILENT\|ggG/ggA\|G452\|684\|GPSM2\|protein_coding\|CODING\|ENST00000406462\|)
cdbdac66d6b5 Uploaded jjohnson parents: diff changeset	7