Counting number of reads affected by N's in CGIAR

I work on plant species. I am using GATK on variant discovery in RNAseq data.
I am not able to decide whether I should use option --filter_reads_with_N_cigar or
What do you suggest?

I Would like to count the number of reads affected by N's in the CIGAR? Could you please suggest any tool?

Secondly, I am using Haplotype Caller for variant discovery. It is running very slow (on 12 CPU).
Is it okay to use UnifiedGenotyper instead of Haplotype Caller on RNAseq data?



Sign In or Register to comment.