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Issues list

Consoldiate the two gatk haplotype caller tools good intro project
#407 opened Sep 12, 2018 by susannasiebert
Use MultiQC to summarize QC workflow
#99 opened Mar 10, 2017 by jasonwalker80
Remove unnecessary pindel index good intro project
#104 opened Mar 22, 2017 by jasonwalker80
Setup a travis-ci framework that runs CWL test.
#116 opened Mar 29, 2017 by jasonwalker80
2
Investigate vt as VCF normalization replacement for LeftAlignAndTrimIndels
#145 opened Apr 12, 2017 by jasonwalker80
Add LOH calls enhancement
#152 opened Apr 18, 2017 by jasonwalker80
1
Combine picard bam_to_fastq steps.
#160 opened Apr 27, 2017 by jasonwalker80
Generate raw count files using prepDE.py
#185 opened Jul 5, 2017 by jasonwalker80
Investigate a more generic way of defining sequence metadata enhancement
#188 opened Jul 13, 2017 by jasonwalker80
1
Add a reference cache for Samtools CRAM support
#205 opened Sep 22, 2017 by jasonwalker80
2
Update hotspot list
#285 opened Jun 8, 2018 by jasonwalker80
1
More comprehensive panel of normals
#286 opened Jun 8, 2018 by jasonwalker80
CWL workflow for building reference indices
#49 opened Dec 13, 2016 by jasonwalker80
2
Optional FLT3-ITD focused variant call process enhancement
#287 opened Jun 8, 2018 by jasonwalker80
Update/refactor cat tools enhancement
#422 opened Sep 12, 2018 by johnegarza
Consolidate steps that are repeatedly used together good intro project
#444 opened Sep 13, 2018 by johnegarza
1
Resolve merge_bams tool
#459 opened Sep 18, 2018 by johnegarza
2
BQSR should support a file of intervals. good intro project
#493 opened Nov 7, 2018 by tmooney
@apaul7
Input flattening failure
#499 opened Nov 21, 2018 by johnegarza
Ensuring unique output names
#500 opened Nov 21, 2018 by johnegarza
1
Retain read trimming log and/or summary good intro project
#525 opened Dec 18, 2018 by jasonwalker80
merge causing shortcutting issues
#526 opened Dec 18, 2018 by zlskidmore
5
Create QC-only workflows for WGS, WES and RNA-seq on hold
#551 opened Jan 29, 2019 by jasonwalker80
Increase performance and reliability of VEP
#565 opened Feb 11, 2019 by jasonwalker80
3
filter_vcf_depth.cwl problems handling DNPs?
#1081 opened Nov 26, 2022 by zlskidmore
1
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