I have a question when I analysis Whole-exome sequencing data. I mapping data with BWA as pipeline described. However, it spend long time to mapping with BWA.
So, counld I use bam files from HISAT2 as input to call snp/indels with GATK 4.1.9 version?
Sorry if I miss something important, I am pretty new in using GATK.
Thanks in advance for your time.
Please sign in to leave a comment.