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Hg19 and hg38 from same workflow version - #19

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NagaComBio wants to merge 49 commits into

masterfrom

hg38

Open

Hg19 and hg38 from same workflow version#19
NagaComBio wants to merge 49 commits into
masterfrom
hg38

Commits on Jan 27, 2020
- Adapted indelCallingWorkflow to work for GRCh38. Main changes: Adaptation of analysisIndelCalling.xml with paths to GRCh38 directories, Changing tool code that required data that is not available …
  
  Holtkamp
  authored and
  NagaComBio
  committed
  dd083fd
- Added hg38 REFERENCE_GENOME and INDEX_PREFIX to config file
  
  Holtkamp
  authored and
  NagaComBio
  committed
  5198ab6
- hg38 reference directory typo
  NagaComBio
  committed
  cb34845
- Updating hg38DatabasesDirectory
  NagaComBio
  committed
  bff626e
- TiNDA updated for hg38; Added clustering with raw filters
  NagaComBio
  committed
  7815c9a
- reading raw bgzip file
  NagaComBio
  committed
  597ae75
Commits on Jan 7, 2021
- Indel calling from CRAM files
  NagaComBio
  committed
  0427748
Commits on Feb 11, 2021
- Moving files to ngs_share
  NagaComBio
  committed
  db4044c
Commits on Mar 1, 2021
- Merging main branch
  NagaComBio
  committed
  686a65f
- Moving GRCh38 config to a separate XML
  NagaComBio
  committed
  2a1523b
Commits on Mar 3, 2021
- Changing chr column
  NagaComBio
  committed
  5ac9468
- Removing annovar and bias analysis in sample swap
  NagaComBio
  committed
  f5e9f8b
- Removing unused variables
  NagaComBio
  committed
  b32f561
- Analysis bam header for hg19
  NagaComBio
  committed
  517f2f7
- Blacklist/selfchain only for hg19
  NagaComBio
  committed
  05d0c36
- Max AF to 5% for local control filtering in nocontrol
  NagaComBio
  committed
  627df27
- Adding a WES local control for hg38
  NagaComBio
  committed
  2deb979
- Adjusting gnomad variable
  NagaComBio
  committed
  6b6cf39
- Updating GRCh38 XML
  NagaComBio
  committed
  e2ee87e
- Analysing bam header for hg19
  NagaComBio
  committed
  0471b16
- Fixing typo
  NagaComBio
  committed
  08dec0d
- Removing bias analysis scripts from the repo
  NagaComBio
  committed
  ef7c1a7
Commits on Mar 5, 2021
- Passing the max MAF values to confidence annotation
  NagaComBio
  committed
  6247724
Commits on Mar 19, 2021
- Sorting chrs alphanumerically
  NagaComBio
  committed
  064d592
Commits on Apr 22, 2021
- Nocontrol: 1000genomes - Using AF for filtering instead of EUR_AF
  NagaComBio
  committed
  7024ae7
- Nocontrol filtering: removed commented lines
  NagaComBio
  committed
  7067082
- Reworking the gnomAD and localcontrol variable names
  NagaComBio
  committed
  8a92cd9
Commits on Apr 30, 2021
- Merge branch 'master' into hg38
  NagaComBio
  committed
  c32000b
Commits on Oct 1, 2021
- Increasing the mem requirement
  NagaComBio
  committed
  b06fdbe
Commits on Oct 18, 2021
- Adding chr_prefix for hg38 chrs
  NagaComBio
  committed
  849d77d
Commits on Apr 29, 2022
- Fix column swap bug for nocontrol workflow
  NagaComBio
  committed
  6220c3b
- Update ngs_share path
  NagaComBio
  committed
  41f1d64
Commits on May 24, 2022
- Resource update
  NagaComBio
  committed
  e2b1e59
Commits on May 25, 2022
- Update confidence scoring based on SeqC2, runlowmaf
  NagaComBio
  committed
  3c8effa
Commits on Jul 1, 2022
- Merge branch 'master' into hg38
  NagaComBio
  committed
  8be0cd0
Commits on Sep 16, 2022
- Removing tVAF from penalities & alleleBias to -1
  NagaComBio
  committed
  2394ac0
Commits on Oct 6, 2022
- Upgrade to gencodev39 for hg38
  NagaComBio
  committed
  b282b66
Commits on Nov 7, 2022
- GnomAD and local control based confidence annotation
  NagaComBio
  committed
  219ada5
- Update Readme
  NagaComBio
  committed
  c7bb74f
- Bug fix
  NagaComBio
  committed
  9f57365
Commits on Mar 20, 2023
- Reverting SNP based confidence scoring
  NagaComBio
  committed
  05776cc
- Update reference
  NagaComBio
  committed
  9a2ee42
- Update PLATYPUS_PARAMS
  NagaComBio
  committed
  6b206e2
Commits on Jan 24, 2024
- Merge branch 'master' into hg38
  NagaComBio
  committed
  7bfc634
- Update README.md
  NagaComBio
  committed
  61d12f4
- Creating helper functions
  NagaComBio
  committed
  331e123
- Moving backticks to system cmd
  NagaComBio
  committed
  e4f9c9b
Commits on Jan 26, 2024
- Moving FREQ from filter to MAFCommon flag in info
  NagaComBio
  committed
  cdd1988
- Add more annotations options for reference genome
  NagaComBio
  committed
  4a2b713

Commits

Commits on Jan 27, 2020

Commits on Jan 7, 2021

Commits on Feb 11, 2021

Commits on Mar 1, 2021

Commits on Mar 3, 2021

Commits on Mar 5, 2021

Commits on Mar 19, 2021

Commits on Apr 22, 2021

Commits on Apr 30, 2021

Commits on Oct 1, 2021

Commits on Oct 18, 2021

Commits on Apr 29, 2022

Commits on May 24, 2022

Commits on May 25, 2022

Commits on Jul 1, 2022

Commits on Sep 16, 2022

Commits on Oct 6, 2022

Commits on Nov 7, 2022

Commits on Mar 20, 2023

Commits on Jan 24, 2024

Commits on Jan 26, 2024