Changes between Version 2 and Version 3 of SOPs/vcf


Ignore:
Timestamp:
10/16/13 11:43:54 (11 years ago)
Author:
gbell
Comment:

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  • SOPs/vcf

    v2 v3  
    77As a tabular reference, common tags are as follows:
    88
    9 FILTER field (typically generated by vcf-annotate):
     9'''FILTER''' field (typically generated by vcf-annotate):
    1010
    1111||'''Tag''' || '''Description''' || '''Default threshold''' ||
    … …  
    2323||StrandBias || Min P-value for strand bias || 0.0001 ||
    2424||VDB || Minimum Variant Distance Bias || 0 ||
     25
     26'''INFO''' field (typically generated by bcftools and expanded with vcf-annotate):
     27
     28||'''Tag''' || '''Description''' || '''More details''' ||
     29||AC || Allele count in genotypes ||  ||
     30||AC1 || Max-likelihood estimate of the first ALT allele count (no HWE assumption) ||  ||
     31||AF1 || Max-likelihood estimate of the first ALT allele frequency (assuming HWE) ||  ||
     32||AN || Total number of alleles in called genotypes ||  ||
     33||CGT || The most probable constrained genotype configuration in the trio ||  ||
     34||CLR || Log ratio of genotype likelihoods with and without the constraint ||  ||
     35||DP || Raw read depth ||  ||
     36||DP4 || # high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases ||  ||
     37||FQ || Phred probability of all samples being the same ||  ||
     38||G3 || ML estimate of genotype frequencies ||  ||
     39||HWE || Hardy-Weinberg equilibrium test (PMID:15789306) ||  ||
     40||ICF || Inbreeding coefficient F ||  ||
     41||INDEL || Indicates that the variant is an INDEL. ||  ||
     42||IS || Maximum number of reads supporting an indel and fraction of indel reads ||  ||
     43||MDV || Maximum number of high-quality nonRef reads in samples ||  ||
     44||MQ || Root-mean-square mapping quality of covering reads ||  ||
     45||PC2 || Phred probability of the nonRef allele frequency in group1 samples being larger (, smaller) than in group2. ||  ||
     46||PCHI2 || Posterior weighted chi2 P-value for testing the association between group1 and group2 samples. ||  ||
     47||PR || # permutations yielding a smaller PCHI2. ||  ||
     48||PV4 || P-values for strand bias, baseQ bias, mapQ bias and tail distance bias ||  ||
     49||QBD || Quality by Depth: QUAL/#reads ||  ||
     50||QCHI2 || Phred scaled PCHI2. ||  ||
     51||RPB || Read Position Bias ||  ||
     52||SF || Source File (index to sourceFiles, f when filtered) ||  ||
     53||TYPE || Variant type ||  ||
     54||UGT || The most probable unconstrained genotype configuration in the trio ||  ||
     55||VDB || Variant Distance Bias (v2) for filtering splice-site artefacts in RNA-seq data. ||  ||
     56