Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

XS tag in SAM file



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    Jason Cerrato

    Hi Stella,

    Happy to see if we can help here.


    1. I don't know the meaning of XS tag.

    "Added tags include the aligner-specific XS tag that marks secondary alignment scores in XS:i:# format." link

    "Because the ATTRIBUTES_TO_RETAIN option is set to X0, any aligner-specific tags that are literally X0 will carryover to the merged BAM. BWA-MEM does not output such a tag but does output XS and XA tags for suboptimal alignment score and alternative hits, respectively. " link

    2. How does it affect the post-steps (ex. variant calling, HLA typing, SV detect etc.) when there is no XS tag?

    This forum post might help in answering this question.


    I will speak to a colleague to get you assistance on question 3.

    Kind regards,


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    Hi Jason, 

    I appreciate your reply. 

    Sincerely yours,



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