1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
|
##fileformat=VCFv4.1
##Goby=development (20130411170529)
##FieldGroupAssociations=CHROM=genomic-coordinate,CHROM=cross-sample-field,POS=genomic-coordinate,POS=cross-sample-field,ID=external-identifiers,ID=cross-sample-field,REF=cross-sample-field,ALT=cross-sample-field,QUAL=cross-sample-field,FILTER=cross-sample-field,INFO=cross-sample-field,INFO/BIOMART_COORDS=cross-sample-field,INFO/INDEL=cross-sample-field,INFO/INDEL=indel,INFO/Somatic-P-value(Fisher)[JWZBMNN-PR-02-254-Tumor]=cross-sample-field,INFO/Somatic-P-value(Fisher)[JWZBMNN-PR-02-254-Tumor]=p-value,INFO/Somatic-P-value(Fisher)[JWZBMNN-PR-02-254-Tumor]=statistic,INFO/Somatic-P-value(Fisher)[JWZBMNN-PR-02-254-Tumor]=indexed,FORMAT/GT=genotype,FORMAT/BC=base-calls,FORMAT/GB=good-bases,FORMAT/FB=failed-bases,
##INFO=<ID=BIOMART_COORDS,Number=1,Type=String,Description="Coordinates formatted for use with IGV.">
##INFO=<ID=INDEL,Number=1,Type=Flag,Description="Indicates that the variation is an indel.">
##INFO=<ID=Somatic-P-value(Fisher)[JWZBMNN-PR-02-254-Tumor],Number=1,Type=Float,Description="P-value that a variation is somatic in this particular sample, compared to other germline samples (e.g., germline skin, or mother/father).">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=BC,Number=5,Type=String,Description="Base counts in format A=?;T=?;C=?;G=?;N=?.">
##FORMAT=<ID=GB,Number=1,Type=String,Description="Number of bases that pass base filters in this sample, or ignore string.">
##FORMAT=<ID=FB,Number=1,Type=String,Description="Number of bases that failed base filters in this sample, or ignore string.">
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Allele|Gene|Feature|Feature_type|Consequence|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|HGNC|DISTANCE|CELL_TYPE">
##INFO=<ID=GENE,Number=1,Type=String,Description="Ensembl gene identifier">
##INFO=<ID=GENE_NAME,Number=1,Type=String,Description="Gene name">
##source_20130313.1=vcf-annotate(-1, set by base.pm) -a /ref-start-end-gene-hgnc-sorted.tsv.gz -d /scratchLocal/gobyweb/tmp/238846.2.rascals.q/attributes.lst -c CHROM,FROM,TO,INFO/GENE,INFO/GENE_NAME
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT KABGEHR-PR-02-254-Normal JWZBMNN-PR-02-254-Tumor
1 40714010 . G A . . BIOMART_COORDS=1:40714010-40714010;Somatic-P-value(Fisher)[JWZBMNN-PR-02-254-Tumor]=1.0;CSQ=A|ENSG00000188800|ENST00000372766|Transcript|intron_variant|||||||TMCO2||,A|ENSG00000188800|ENST00000468258|Transcript|intron_variant&nc_transcript_variant|||||||TMCO2|| GT:BC:GB:FB 0/1:A=11,G=22:33:2 0/1:A=5,G=22:27:0
1 40724030 . AG A- . . BIOMART_COORDS=1:40724030-40724030;INDEL;Somatic-P-value(Fisher)[JWZBMNN-PR-02-254-Tumor]=0.03432494279176201;CSQ=A-|ENSG00000084073|ENST00000479131|Transcript|non_coding_exon_variant&nc_transcript_variant|123-124||||||ZMPSTE24||,A-|ENSG00000084073|ENST00000372759|Transcript|missense_variant&coding_sequence_variant|252-253|87-88|29-30|TV/TX|acAGtg/acA-tg||ZMPSTE24||,A-|ENSG00000231296|ENST00000447743|Transcript|downstream_gene_variant||||||||4313|,A-|ENSG00000259943|ENST00000567508|Transcript|upstream_gene_variant||||||||391|,A-|ENSG00000084073|ENST00000472583|Transcript|non_coding_exon_variant&nc_transcript_variant|120-121||||||ZMPSTE24|| GT:BC:GB:FB 0/1:A=168,A-=1:169:1 0/1:A=187,A-=11:198:3
1 40737516 . T G . . BIOMART_COORDS=1:40737516-40737516;Somatic-P-value(Fisher)[JWZBMNN-PR-02-254-Tumor]=1.0;CSQ=G|ENSG00000084073|ENST00000372759|Transcript|intron_variant|||||||ZMPSTE24||,G|ENSG00000084073|ENST00000472583|Transcript|downstream_gene_variant|||||||ZMPSTE24|4008| GT:BC:GB:FB 1/1:G=86:86:0 1/1:G=98:98:0
1 40737589 . T C . . BIOMART_COORDS=1:40737589-40737589;Somatic-P-value(Fisher)[JWZBMNN-PR-02-254-Tumor]=1.0;CSQ=C|ENSG00000084073|ENST00000372759|Transcript|synonymous_variant|816|651|217|D|gaT/gaC||ZMPSTE24||,C|ENSG00000084073|ENST00000472583|Transcript|downstream_gene_variant|||||||ZMPSTE24|4081| GT:BC:GB:FB 0/1:T=118,C=95:213:9 0/1:T=120,C=107:227:11
1 40758348 . C A . . BIOMART_COORDS=1:40758348-40758348;Somatic-P-value(Fisher)[JWZBMNN-PR-02-254-Tumor]=0.1666666666666667;CSQ=A|ENSG00000084073|ENST00000372759|Transcript|3_prime_UTR_variant|1600||||||ZMPSTE24||,A|ENSG00000084073|ENST00000474142|Transcript|downstream_gene_variant|||||||ZMPSTE24|55| GT:BC:GB:FB 0/0:C=265:265:0 0/1:A=5,C=231:236:1
|
