Changes between Version 6 and Version 7 of SOPs/vcf


Ignore:
Timestamp:
10/16/13 15:56:46 (11 years ago)
Author:
gbell
Comment:

--

Legend:

Unmodified
Added
Removed
Modified

  • SOPs/vcf

    v6 v7  
    3838||CLR || Log ratio of genotype likelihoods with and without the constraint ||  ||
    3939||DP || Raw read depth || For multiple-sample VCFs, the sum for all samples ||
    40 ||DP4 || # high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases ||  ||
     40||DP4 || Number of high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases ||  ||
    4141||FQ || Phred probability of all samples being the same ||  ||
    4242||G3 || ML estimate of genotype frequencies ||  ||
    … …  
    4949||PC2 || Phred probability of the nonRef allele frequency in group1 samples being larger (, smaller) than in group2. ||  ||
    5050||PCHI2 || Posterior weighted chi2 P-value for testing the association between group1 and group2 samples. ||  ||
    51 ||PR || # permutations yielding a smaller PCHI2. ||  ||
     51||PR || Number of permutations yielding a smaller PCHI2. ||  ||
    5252||PV4 || P-values for strand bias, baseQ bias, mapQ bias and tail distance bias ||  ||
    5353||QBD || Quality by Depth: QUAL/#reads ||  ||