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arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
MIT License
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Output BAM with tags to associate reads back to SV calls? #373

Open nh13 opened 2 years ago

nh13 commented 2 years ago

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 commented 2 years ago

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.

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.

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