ngs-bits icon indicating copy to clipboard operation
ngs-bits copied to clipboard

Published 20 hours ago • verified publisher icon imgag

convert legacy data to masked GRCh38

Open marc-sturm opened this issue 10 months ago • 1 comments

  • [x] convert BAMs of legacy samples to CRAM for diagnostics (WGS and WES) when GRCh38 with false duplications masked was used
  • [ ] correct for GRCh38 with false duplications not masked
  • [ ] remove legacy BAM files when CRAM/CRAI files are present und have the right size and valid samtools quickcheck
  • [ ] re-create coverage profiles for CNV calling
    • [ ] re-do CNP calling

marc-sturm avatar Aug 29 '23 07:08 marc-sturm

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

marc-sturm avatar Sep 15 '23 11:09 marc-sturm