How does gatk deal with bam XA tag when calling variations?

Hello,

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!

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by Sheila

Issue Number
2471
State
closed
Last Updated
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sooheelee

Best Answer

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @liujing251614
    Hi,

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

    -Sheila

  • Yeah, thank you~

  • I get it, thanks a lot!

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