Difference between revisions of "VCF format"
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| + | :VCF format (*.vcf) | ||
| + | ;Element type | ||
| + | :{{Type link|track}} | ||
| + | ;Plugin | ||
| + | :[[Ru.biosoft.bsa (plugin)|ru.biosoft.bsa (Bio-sequences analyses plugin)]] | ||
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=== VCF (Variant call format) === | === VCF (Variant call format) === | ||
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[[Category:File formats]] | [[Category:File formats]] | ||
| + | [[Category:Autogenerated pages]] | ||
Latest revision as of 16:40, 17 May 2013
- File format title
- VCF format (*.vcf)
- Element type
track
- Plugin
- ru.biosoft.bsa (Bio-sequences analyses plugin)
[edit] VCF (Variant call format)
VCF is a text file format (most likely stored in a compressed manner). It contains meta-information lines, a header line, and then data lines each containing information about a position in the genome.
[edit] Example
##fileformat=VCFv4.0 ##fileDate=20090805 ##source=myImputationProgramV3.1 ##reference=1000GenomesPilot-NCBI36 ##phasing=partial ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> ##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency"> ##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele"> ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129"> ##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership"> ##FILTER=<ID=q10,Description="Quality below 10"> ##FILTER=<ID=s50,Description="Less than 50% of samples have data"> #CHROM POS ID REF ALT QUAL FILTER INFO 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB 20 1230237 . T . 47 PASS NS=3;DP=13;AA=T 20 1234567 microsat1 GTCT G,GTACT 50 PASS NS=3;DP=9;AA=G
