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

...