Hi,
I want to know when call variants by GATK pipeline, you call SNPs and InDels simultaneously (use -glm BOTH) or separately in two rounds of run. I noticed that considering BAQ will decrease the performance of calling InDels. But how can I deal with the conflicted alleles generated by SNPs and their nearby InDels?
Best,
SK
I want to know when call variants by GATK pipeline, you call SNPs and InDels simultaneously (use -glm BOTH) or separately in two rounds of run. I noticed that considering BAQ will decrease the performance of calling InDels. But how can I deal with the conflicted alleles generated by SNPs and their nearby InDels?
Best,
SK