Attention:
The frontline support team will be unavailable to answer questions until May27th 2019. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!

ProduceBeagleInput feature request

tommycarstensentommycarstensen United KingdomMember ✭✭✭

After UnifiedGenotyper --genotype_likelihoods_model BOTH I have this INDEL: 1 10146 . AC A 22089 .

After ApplyRecalibration --mode SNP I still have this INDEL, however it is not marked as PASSed: 1 10146 . AC A 22089 .

If I apply ProduceBeagleInput directly to the AR output, then that INDEL is included in the PBI output.

You were kind enough to disallow CombineVariants from setting a FILTER value of PASS (http://gatkforums.broadinstitute.org/discussion/2647/combinevariants-removefilter-feature-request). As a low priority, can you give the option to disallow PBI from using variants, which do not have a FILTER value of PASS (or whatever value decided by the user)?

Thank you for a good tool kit.

Sign In or Register to comment.