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| Variant Call Format ： ウィキペディア英語版 |
Variant Call Format
The Variant Call Format (VCF) specifies the format of a text file used in bioinformatics for storing gene sequence variations. The format has been developed with the advent of large-scale genotyping and DNA sequencing projects, such as the 1000 Genomes Project. Existing formats for genetic data such as General feature format (GFF) stored all of the genetic data, much of which is redundant because it will be shared across the genomes. By using the variant call format only the variations need to be stored along with a reference genome.
The standard is currently in version 4.2,〔(【引用サイトリンク】title=VCF Specification )〕〔(【引用サイトリンク】title=Specifications of SAM/BAM and related high-throughput sequencing file formats )〕 although the 1000 Genomes Project has developed their own specification for structural variations such as duplications, which are not easily accommodated into the existing schema.〔(【引用サイトリンク】title=Encoding Structural Variants in VCF (Variant Call Format) version 4.0 | 1000 Genomes )〕 A set of tools is also available for editing and manipulating the files.〔(【引用サイトリンク】title=VCFtools from SourceForge.net )〕
==Example==
##fileformat=VCFv4.0
##fileDate=20110705
##reference=1000GenomesPilot-NCBI37
##phasing=partial
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##FILTER=
##FILTER=
##FORMAT=
##FORMAT=
##FORMAT=
##FORMAT=
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1 Sample2 Sample3
2 4370 rs6057 G A 29 . NS=2;DP=13;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:52,51 1|0:48:8:51,51 1/1:43:5:.,.
2 7330 . T A 3 q10 NS=5;DP=12;AF=0.017 GT:GQ:DP:HQ 0|0:46:3:58,50 0|1:3:5:65,3 0/0:41:3
2 110696 rs6055 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4
2 130237 . T . 47 . NS=2;DP=16;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:56,51 0/0:61:2
2 134567 microsat1 GTCT G,GTACT 50 PASS NS=2;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3
抄文引用元・出典: フリー百科事典『 ウィキペディア（Wikipedia）』
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