I have been using gtcheck functionality of bcftools to calculate genotype
discordance between 2 samples, and used the -a option to print this
information at all sites. The command I used is:
./gatk/bcftools/bcftools gtcheck -G 1 -g $file1.vcf.gz $file2.vcf.bgz -a -S
$samp1
And, the header header of the output file I get is below. How is the column
[6] calculated; and why is it outputting the Query PLs and not the Query
GT.
# [1]SC, Site by Site Comparison [2]Chromosome [3]Position
[4]-g alleles [5]-g GT (LP6005441-DNA_E02) [6]match log
LK [7]Query alleles [8-]Query PLs (LP6005441-DNA_E02)
Also, how does it calculate the genotype concordance, which sites does it
consider when doing this; it seems to be dropping quite a lot of sites,
which ones are those? Also, what is the expected discordance between 2
random samples?
Thanks,
Arti
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