Is there similar functionality as EMIT_ALL_SITES for Indels?
Posted in Ask the GATK team | Last updated on 2013-09-06 12:50:13

Comments (4)

Hello, I noticed that you can use emit_all_sites in UnifiedGenotyper to gather information on alternate alleles at every base provided in the interval file. Is there a way to do this same process but with indels? I want to pass in an interval list of indel locations and a bam file and for every site in the interval list get number of reads supporting the indel and number of reference. Thanks you.

Return to top Comment on this article in the forum