GraphAligner is a great tool (thank you). I've noticed that the alignments that GraphAligner outputs never include the base-level quality scores from the aligned reads. I understand that this is expected behavior, and I'm not asking for it to be changed, but I'm wondering if there's a recommended way to pull these scores from the aligned reads and add them into the GAM output by GraphAligner. I want to do this because variant callers I work with require the qual scores, and I imagine others have encountered this issue too.
The obvious answer would be to index the clipped reads to match the gam and then lift over the qual scores, but the --corrected-clipped-out flag outputs reads in fasta, so no qual scores. Any advice or hints would be appreciated.
GraphAligner is a great tool (thank you). I've noticed that the alignments that GraphAligner outputs never include the base-level quality scores from the aligned reads. I understand that this is expected behavior, and I'm not asking for it to be changed, but I'm wondering if there's a recommended way to pull these scores from the aligned reads and add them into the GAM output by GraphAligner. I want to do this because variant callers I work with require the qual scores, and I imagine others have encountered this issue too.
The obvious answer would be to index the clipped reads to match the gam and then lift over the qual scores, but the
--corrected-clipped-outflag outputs reads in fasta, so no qual scores. Any advice or hints would be appreciated.Thanks!!