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Hg19 and hg38 analysis from same workflow branch #8

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Hg19 and hg38 analysis from same workflow branch #8

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Commits on Aug 19, 2019

  1. Removing ExAC and EVS from annotation and no-control filtering

    @NagaComBio
    NagaComBio committed Aug 19, 2019
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Commits on Oct 11, 2019

  1. Removing DUKE, DAC and HiSeqDepth based confidence annotaions

    @NagaComBio
    NagaComBio committed Oct 11, 2019
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  2. Removing getRefGenomeAndChrPrefixFromHeader functions

    @NagaComBio
    NagaComBio committed Oct 11, 2019
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  3. Updating annotation file paths to hg38 directory

    @NagaComBio
    NagaComBio committed Oct 11, 2019
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Commits on Jan 21, 2020

  1. Removing the hg38 encode blacklist filter

    @NagaComBio
    NagaComBio committed Jan 21, 2020
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Commits on Jan 7, 2021

  1. Variant calling from CRAM files

    @NagaComBio
    NagaComBio committed Jan 7, 2021
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Commits on Feb 11, 2021

  1. Checking for nonREFnonALT in BoolCounter class

    @NagaComBio
    NagaComBio committed Feb 11, 2021
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  2. updating pysam to 0.16.0.1

    @NagaComBio
    NagaComBio committed Feb 11, 2021
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  3. Moving files to ngs_share

    @NagaComBio
    NagaComBio committed Feb 11, 2021
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Commits on Mar 11, 2021

  1. Updating BoolCounter class

    @NagaComBio
    NagaComBio committed Mar 11, 2021
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  2. REF name via BAM header

    @NagaComBio
    NagaComBio committed Mar 11, 2021
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  3. Reverting generic xml to hg19

    @NagaComBio
    NagaComBio committed Mar 11, 2021
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  4. New xml for GRCh38 files

    @NagaComBio
    NagaComBio committed Mar 11, 2021
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  5. chrLength file with 'chr' prefix

    @NagaComBio
    NagaComBio committed Mar 11, 2021
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Commits on Mar 16, 2021

  1. Removing hard-coded header parsing

    @NagaComBio
    NagaComBio committed Mar 16, 2021
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  2. Liftover local control for hg38 WES and WGS

    @NagaComBio
    NagaComBio committed Mar 16, 2021
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  3. hg19 specific annotations

    @NagaComBio
    NagaComBio committed Mar 16, 2021
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  4. User defined threshold-based 'SNP_support_germline' annotations

    @NagaComBio
    NagaComBio committed Mar 16, 2021
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  5. Removed extra spaces

    @NagaComBio
    NagaComBio committed Mar 16, 2021
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  6. Merge branch 'master' into hg38 

    Conflicts:
	resources/analysisTools/snvPipeline/confidenceAnnotation_SNVs.py
	resources/analysisTools/snvPipeline/filter_PEoverlap.py
	resources/analysisTools/snvPipeline/snvAnnotation.sh
	resources/configurationFiles/analysisSNVCalling.xml
    @NagaComBio
    NagaComBio committed Mar 16, 2021
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Commits on Apr 26, 2021

  1. Uncommenting reference detection

    @NagaComBio
    NagaComBio committed Apr 26, 2021
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Commits on Apr 30, 2021

  1. updating refgenome help

    @NagaComBio
    NagaComBio committed Apr 30, 2021
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  2. Raise error: unknown alignment suffix

    @NagaComBio
    NagaComBio committed Apr 30, 2021
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  3. Reformatting in_dbSNPcounter.pl

    @NagaComBio
    NagaComBio committed Apr 30, 2021
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  4. Reformatting IMD R file

    @NagaComBio
    NagaComBio committed Apr 30, 2021
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Commits on Sep 29, 2021

  1. Increasing the mem requirement

    @NagaComBio
    NagaComBio committed Sep 29, 2021
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Commits on Oct 22, 2021

  1. safer IO for in_dbSNPcounter.pl

    @NagaComBio
    NagaComBio committed Oct 22, 2021
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Commits on May 4, 2022

  1. Add variant calling in HLA/ALT contigs

    @NagaComBio
    NagaComBio committed May 4, 2022
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  2. Update ngs_share path

    @NagaComBio
    NagaComBio committed May 4, 2022
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Commits on May 30, 2022

  1. Remove RE/MAP from hg38 penalties

    @NagaComBio
    NagaComBio committed May 30, 2022
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Commits on Jul 8, 2022

  1. Add m2e2,HLA/ALT mappability files

    @NagaComBio
    NagaComBio committed Jul 8, 2022
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  2. Merge branch 'mappability branch' into hg38

    @NagaComBio
    NagaComBio committed Jul 8, 2022
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Commits on Sep 16, 2022

  1. Fix the diagnostic plots for GRCh38

    @NagaComBio
    NagaComBio committed Sep 16, 2022
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  2. Remove the quote for RAW_SNV_FILTER_OPTIONS

    @NagaComBio
    NagaComBio committed Sep 16, 2022
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Commits on Oct 6, 2022

  1. Upgrade to gencodev39 for hg38

    @NagaComBio
    NagaComBio committed Oct 6, 2022
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Commits on Oct 27, 2022

  1. Merge branch 'master' into hg38

    @NagaComBio
    NagaComBio committed Oct 27, 2022
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Commits on Nov 7, 2022

  1. Bug fix with dbSNP counter

    @NagaComBio
    NagaComBio committed Nov 7, 2022
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  2. Update WGS local control

    @NagaComBio
    NagaComBio committed Nov 7, 2022
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  3. hg38: Add local control and gnomAD based confidence annotation

    @NagaComBio
    NagaComBio committed Nov 7, 2022
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  4. Update README

    @NagaComBio
    NagaComBio committed Nov 7, 2022
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  5. Exempt classification with FREQ

    @NagaComBio
    NagaComBio committed Nov 7, 2022
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Commits on Mar 20, 2023

  1. Reverting SNP based confidence scoring

    @NagaComBio
    NagaComBio committed Mar 20, 2023
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  2. Add exception for 'N' in createErrorPlots.py

    @NagaComBio
    NagaComBio committed Mar 20, 2023
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  3. Remove NA values in quantile calculation

    @NagaComBio
    NagaComBio committed Mar 20, 2023
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  4. Update reference

    @NagaComBio
    NagaComBio committed Mar 20, 2023
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  5. Update raw_filter_punishment in accordance with RAW_SNV_FILTER_OPTIONS

    @NagaComBio
    NagaComBio committed Mar 20, 2023
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Commits on Mar 23, 2023

  1. Move python env

    @NagaComBio
    NagaComBio committed Mar 23, 2023
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Commits on Jun 12, 2023

  1. Update virtual env path

    @NagaComBio
    NagaComBio committed Jun 12, 2023
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  2. XML comments to description

    @NagaComBio
    NagaComBio committed Jun 12, 2023
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  3. Merge branch 'master' into hg38 

    Conflicts:
	README.md
	resources/analysisTools/snvPipeline/environments/tbi-lsf-cluster.sh
	resources/analysisTools/snvPipeline/filter_PEoverlap.py
	resources/configurationFiles/analysisSNVCalling.xml
    @NagaComBio
    NagaComBio committed Jun 12, 2023
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  4. Minor update

    @NagaComBio
    NagaComBio committed Jun 12, 2023
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  5. Update readme with hg38 calls

    @NagaComBio
    NagaComBio committed Jun 12, 2023
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Commits on Jun 27, 2023

  1. Fixing the missed conflict

    @NagaComBio
    NagaComBio committed Jun 27, 2023
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