SvPileup writes a query-grouped BAM, but AggregateSvPileup requires a coordinate sorted and index BAM

fulcrumgenomics / fgsv

Tools to gather evidence for structural variation via breakpoint detection.

MIT License

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SvPileup writes a query-grouped BAM, but AggregateSvPileup requires a coordinate sorted and index BAM #15

Closed nh13 closed 1 year ago

nh13 commented 2 years ago

This is not clarified in the AggregateSvPileup documentation

tfenne commented 1 year ago

AggregateSvPileup wants the same set of reads that were fed into SvPileup, not it's output. However the documentation is still wrong - it says is must be the same BAM file as used in SvPileup, when what it should say is the same BAM file, except in coordinate sort order.