GATK UnifiedGenotyper pooled sample

[sirmark]

Hi!

How do I use UnifiedGenotyper in pooled samples ?

I have a bam file in which there are 5 individuals for each pool.

do GATK UnifiedGenotyper take into account of pooled sample ?

thank you!

[sirmark]

ok, I have corrected the request, that before was too specific

[vivek_]

As long as the sample names are different in the BAM header, it should be fine.

[sirmark]

--sample_ploidy 5 is the option to use ?

[vivek_]

Just as a general recommendation/warning: if your 50 haploid genomes are truly pooled and then sequenced then the -ploidy 50 is correct. But if your samples are individually barcoded (or sequenced separately) and hence are marked as separate samples in your BAM then that would be incorrect: you should set -ploidy 1 and you'll get in your output your individual genotypes for each sample. - See more at: http://gatkforums.broadinstitute.org....Jkr7fN80.dpuf

Got this off the GATK forum.

I assumed your data was from different individuals in one bam.

[sirmark]

ok, thank you!