Entering edit mode
11.4 years ago
William
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5.2k
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