Genotype And Genotype-likelihood concordance scripts...
With sequencing duplicate pairs...
Usage:
(GT concordance. Output one line per pair. Can be re-ordered to 3x3 table)
GTpairConcordance-new.pl inVcf Pair.list > GTconcordance.out
(GL concordance, estimated with Bayes factor. Output one line per site)
PairGLconcordance.pl inVcf Pair.list Exclude.list > GLconcordance.out
Pair list format (delimited by tab):
P11 P12
P21 P22
...
Exclude list format:
Exclude-sample1
Exclude-sample2
...