Ped File Individual Id Same As Bam Rg Sample Name For Gatk?

Question

[William]

Should the Individual ID in the ped file correspond to a sample name in a BAM file?

I want to analyze a trio using GATK and I need to pass in a ped file to specify the pedigree but I am wondering how GATK matches the right BAMs to the right pedigree individual.

See: http://gatkforums.broadinstitute.org/discussion/37/pedigree-analysis http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_CommandLineGATK.html#--pedigree

Answer 1

[dr.eli.roberson]

Gatk will use rgsm if it is in the bam, but the filename otherwise.