XQ Tag

[MateuszMarynowski]

I saw an XQ tag in the resulting bam, and I can't find what it is anywhere. Could you explain what an XQ tag is?

Because of this tag, the RevertSam tool from gatk does not work and I get this error:

htsjdk.samtools.SAMException: Value for tag XQ is not a String: class java.lang.Integer

Could this tag change the data type from int to string?

[rpetrovski]

It is set when calculated MAPQ is over 60. Cheers. Roman.

…

On Fri, 31 Mar 2023, 14:17 Mateusz Marynowski, ***@***.***> wrote: I saw an XQ tag in the resulting bam, and I can't find what it is anywhere. Could you explain what an XQ tag is? Because of this tag, the RevertSam tool from gatk does not work and I get this error: htsjdk.samtools.SAMException: Value for tag XQ is not a String: class java.lang.Integer Could this tag change the data type from int to string? — Reply to this email directly, view it on GitHub <#52>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAXSY4NJMQ6DWEAJRWYIQWTW63KOZANCNFSM6AAAAAAWOUUWYQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[5im1z]

Hello @MateuszMarynowski , were you able to resolve the issue with RevertSam by any chance? I'd appreciate any pointers. Thank you!

[abhisheknrl]

I have the same issue. Would appreciate if you have found a solution to this issue with RevertSam and XQ tag.

[5im1z]

I ended up running RevertSam with the --RESTORE_HARDCLIPS false flag and it worked for me.

[abhisheknrl]

Thanks! I ended up using another alignment workflow.