Output BAM with tags to associate reads back to SV calls?

[nh13]

Is there a way (or would be difficult) to output a BAM with the reads that contributed to the SV calls, with a SAM tag that identifies which call? This is super useful for debugging calls in IGV. For example, see the GATK HaplotypeCaller assembly BAM output.

[ryanlayer]

That would be useful, but I think the best place fo etc this output would be in SVTyper. We are better able to determine which reads support the SV in the genotyping stage. Check out the ‘-w’ flag in SVTyper.

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On Jan 28, 2022, at 11:19 AM, Nils Homer ***@***.***> wrote:  Is there a way (or would be difficult) to output a BAM with the reads that contributed to the SV calls, with a SAM tag that identifies which call? This is super useful for debugging calls in IGV. For example, see the GATK HaplotypeCaller assembly BAM output. — Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you are subscribed to this thread.