Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
How does gatk deal with bam XA tag when calling variations?
When a read has mutli-hits on a reference genome, the bam file would record mutli positions in XA tag. So, would GATK consider the XA tag when calling variations?
After getting filtered VCF using gatk, I found that some sites were covered by many reads (for example, more than ten). But when I check the bam file in the IGV viewer, these sites didn't have any reads but the consensus sequence was intact. So, I wonder whether GATK also count the reads in the XA tag when calling variations?
Thanks a lot！