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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!


Issue · Github
by Sheila

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  • SheilaSheila Broad InstituteMember, Broadie admin


    I have asked another team mate to respond, as she knows more. But, you may find this thread useful in the meantime.


  • liujing251614liujing251614 ChinaMember

    Yeah, thank you~

  • liujing251614liujing251614 ChinaMember

    I get it, thanks a lot!

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