Changes between Version 1 and Version 2 of SOPs/vcf


Ignore:
Timestamp:
10/16/13 10:28:57 (11 years ago)
Author:
gbell
Comment:

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  • SOPs/vcf

    v1 v2  
    11= Interpreting VCF files =
     2
     3The [http://vcftools.sourceforge.net/specs.html VCF (Variant Call Format) specification] describes most of what you need to know.
     4
     5Tags in the FILTER, INFO, and FORMAT fields are described in the VCF header.
     6
     7As a tabular reference, common tags are as follows:
     8
     9FILTER field (typically generated by vcf-annotate):
     10
     11||'''Tag''' || '''Description''' || '''Default threshold''' ||
     12||BaseQualBias || Min P-value for baseQ bias || 0 ||
     13||EndDistBias || Min P-value for end distance bias || 0.0001 ||
     14||GapWin || Window size for filtering adjacent gaps || 3 ||
     15||MapQualBias || Min P-value for mapQ bias || 0 ||
     16||MaxDP || Maximum read depth || 10000000 ||
     17||MinAB || Minimum number of alternate bases || 2 ||
     18||MinDP || Minimum read depth || 2 ||
     19||MinMQ || Minimum RMS mapping quality for SNPs || 10 ||
     20||Qual || Minimum value of the QUAL field || 10 ||
     21||RefN || Reference base is N || [] ||
     22||SnpGap || SNP within INT bp around a gap to be filtered || 10 ||
     23||StrandBias || Min P-value for strand bias || 0.0001 ||
     24||VDB || Minimum Variant Distance Bias || 0 ||