Sample extraction fails with -O bcf

[rick-heig]

Hello. I compressed chr1 from 1KGP3 (available here ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/)

And checked the file with the following commands :

sav export -O vcf chr1.sav | less

sav export -O bcf chr1.sav | bcftools view | less

This is ok.

Then, for sample extraction and ran the following commands :

sav export -O vcf -i "NA12878,HG00109" chr1.sav | less

which works but,

sav export -O bcf -i "NA12878,HG00109" chr1.sav | bcftools view | less

doesn't work, only the header is shown.

So it seems there is a small bug with the interaction of the -O bcf and -i "sample list" options.

Best regards, Rick

[jonathonl]

Thanks for reporting this. I just pushed some fixes for this (200dfe721a5bdf40c7e0af3bfbb4c2d66970e530 and f79b38b336adbef782e17a7d7cde52808da3d939). Please try the latest from master.