Code

somatic_exome cram version#973

Code

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johnegarza wants to merge 10 commits intogenome:mastergenome/analysis-workflows:masterfrom johnegarza:somatic_exome_cram_readcountjohnegarza/analysis-workflows:somatic_exome_cram_readcountCopy head branch name to clipboard

+353-378

Commits

Commits on Sep 3, 2020

• beginning to modify somatic_exome pipeline for bam_readcount cram support

  johnegarza

  committed
  b067d60

• Merge branch 'master' into somatic_exome_cram_readcount

  johnegarza

  committed
  82b8ee0

Commits on Sep 4, 2020

• Update all parts of workflow to accept cram inputs when possible

  johnegarza

  committed
  275b5c1

• bugfixes

  johnegarza

  committed
  b4d02c5

Commits on Oct 7, 2020

• Merge branch 'master' into somatic_exome_cram_readcount

  johnegarza

  committed
  1f7dc0b

Commits on Dec 4, 2020

• Samtools packaged with mutect is old and can't open cram files

  johnegarza

  committed
  b16fbd5

• Use custom patched version of cnvkit that supports opening crams with a local reference fasta

  johnegarza

  committed
  b77344d

• Use patched version of bam-readcount that supports crams

  johnegarza

  committed
  dbdbb3b

• cleanup

  johnegarza

  committed
  0505632

• Merge branch 'master' into somatic_exome_cram_readcount

  johnegarza

  committed
  8d98d6b