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Commits on Jan 26, 2026

• clean up a couple of rules and add a few notes

  tomsasani

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  91fb426

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Commits on Jan 23, 2026

• updates to scripts for scott ORA processing, minor bumps to bash scripts for variant calling

  tomsasani

  committed
  f23cda4

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Commits on Jan 22, 2026

• hacky method to run on multiple accts and partitions incl cpu and gpu

  tomsasani

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  1a0c905

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Commits on Jan 15, 2026

• hacky bash scripts to decompress scott's ORA files

  tomsasani

  committed
  437aaf5

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Commits on Jan 12, 2026

• add possible parabricks bwa implementation, decrease cpu usage in dv

  tomsasani

  committed
  ca1f9d6

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Commits on Jan 9, 2026

• bump parabricks implementation, add CIDR topup samples to pipeline

  tomsasani

  committed
  465b6bb

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• use parabricks

  tomsasani

  committed
  2b2b758

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Commits on Dec 23, 2025

• missing input in bam2cram conversion

  tomsasani

  committed
  f520ca0

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• bump cram2fastq and fastq2bam

  tomsasani

  committed
  017f58b

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Commits on Dec 19, 2025

• new rules for realignment of CIDR samples

  tomsasani

  committed
  3a09e77

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Commits on Nov 19, 2025

• add pipeline for re-calling with DV

  tomsasani

  committed
  3e5e875

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Commits on Jul 11, 2025

• add separate workflow to genotype GVCFs from genomics DB store

  tomsasani

  committed
  2bdc2e4

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• code to make JSON file with GVCF mapping

  tomsasani

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  9d7e192

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• standalone bash script for adding to genomics db

  tomsasani

  committed
  3ad509f

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• basic code to make sample lists for CEPH and CIDR

  tomsasani

  committed
  48bdca6

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• update code to do an incremental addition of samples to genomics DBs

  tomsasani

  committed
  ef4ed7a

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Commits on Jul 9, 2025

• refactor to joint-genotype all families

  tomsasani

  committed
  bcaa932

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Commits on May 22, 2025

• require index for gvcf before adding to genomicsDB

  tomsasani

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  2de2950

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Commits on May 21, 2025

• normalize gvcf before adding to GenomicsDB

  tomsasani

  committed
  aa87d0d

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• joint-genotype whole chromosomes, add slivar logi

  tomsasani

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  9820536

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Commits on May 16, 2025

• add readme

  tomsasani

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  a368b1b

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• initial commit with smk pipeline and configs

  tomsasani

  committed
  7618627

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