convert legacy data to masked GRCh38 - Githubissues

imgag / ngs-bits

Short-read sequencing tools

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convert legacy data to masked GRCh38 #479

Open marc-sturm opened 11 months ago

marc-sturm commented 11 months ago

Todo:

[x] convert BAMs of legacy samples to CRAM for diagnostics (WGS and WES) when GRCh38 with false duplications masked was used
[x] correct for GRCh38 with false duplications not masked
[ ] re-create coverage profiles for CNV calling
[x] delete BAMs

Pakreatitis control samples used by Andreas:

[ ] convert BAMs of legacy samples to CRAM when GRCh38 with false duplications masked was used
[ ] correct for GRCh38 with false duplications not masked
[ ] re-create coverage profiles for CNV calling
[ ] delete BAMs (when Andreashas published the pancreatitis data)

marc-sturm commented 10 months ago

Implemented tool to fix BAMs that were mapped with a hg38 genome without masked false duplications: https://github.com/imgag/megSAP/blob/master/src/Tools/bam_fix_unmasked_duplications.php