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Issues list

Allow pvactools --percentile-threshold-strategy to be set in immuno.wdl immuno-paper implement before publication of immuno paper
#182 opened Feb 28, 2025 by malachig updated Mar 7, 2025
@susannasiebert
2
Improve selection of variant annotation for the variants.tsv immuno-paper implement before publication of immuno paper
#124 opened Jun 5, 2023 by malachig updated Mar 7, 2025
1
@susannasiebert
7
Update version of bam-readcount used in immuno immuno-paper implement before publication of immuno paper
#179 opened Feb 19, 2025 by malachig updated Mar 7, 2025
@malachig
3
Keep the pvacseq log files as an output immuno-paper implement before publication of immuno paper
#180 opened Feb 27, 2025 by malachig updated Mar 4, 2025
1
@susannasiebert
1
Add HLA typing predictions using tumor RNA-seq data immuno-paper implement before publication of immuno paper
#175 opened Feb 5, 2025 by malachig updated Feb 27, 2025
@evelyn-schmidt
2
Add somalier analysis for the RNA samples analyzed as part of immuno pipeline immuno-paper implement before publication of immuno paper
#164 opened Oct 16, 2024 by malachig updated Feb 27, 2025
@ksinghal28 @JinglunLi1998
Create ROI files that work generically for neoantigen prediction regardless of exome reagent used
#173 opened Jan 31, 2025 by malachig updated Feb 27, 2025
@malachig
1
Add support for configuration of mismatch quality related filters that are applied to each somatic variant caller result
#172 opened Jan 31, 2025 by malachig updated Feb 27, 2025
@ksinghal28
1
Investigate addition of deepsomatic as a new somatic variant caller immuno-paper implement before publication of immuno paper
#177 opened Feb 10, 2025 by malachig updated Feb 27, 2025
@ksinghal28
Add a third HLA typing algorithm that supports DRB3/4/5, DPA1, and DPB1 alleles immuno-paper implement before publication of immuno paper
#171 opened Jan 15, 2025 by malachig updated Feb 27, 2025
@evelyn-schmidt
3
Harmonize indel alignment between bwa-mem and STAR alignments for the purpose of variant allele counting immuno-paper implement before publication of immuno paper
#176 opened Feb 5, 2025 by malachig updated Feb 27, 2025
@malachig
8
Replicate Somalier analysis to include rnaseq bam files in Immuno.wdl immuno-paper implement before publication of immuno paper
#178 opened Feb 12, 2025 by ksinghal28 updated Feb 27, 2025
@ksinghal28 @JinglunLi1998
Adding af_gnomade flag to VEP annotation command enhancement New feature or request
#174 opened Jan 31, 2025 by evelyn-schmidt updated Feb 1, 2025
Correct the HISAT reference index to be a string instead of a file
#166 opened Dec 12, 2024 by malachig updated Dec 12, 2024
use localization_optional when possible performance optimizations of run time adn/or cost
#64 opened Aug 9, 2022 by chrisamiller updated Oct 15, 2024
4
Troubleshoot failures during localization step
#154 opened Sep 3, 2024 by malachig updated Sep 5, 2024
1
Create a tool that aggregates and prioritizes/filters fusion neoantigens
#151 opened Aug 2, 2024 by malachig updated Aug 2, 2024
1
Add HLA LOH analysis to immuno workflow
#146 opened Mar 7, 2024 by malachig updated Mar 7, 2024
Investigate inconsistent variant results from varscan when using localization_optional bug Something isn't working performance optimizations of run time adn/or cost
#109 opened Apr 12, 2023 by malachig updated Feb 28, 2024
@malachig
2
Giving pVACseq output files unique names enhancement New feature or request
#140 opened Dec 7, 2023 by evelyn-schmidt updated Dec 7, 2023
pvacseq/pvacfuse hangs and fails to complete
#131 opened Sep 12, 2023 by rkageyama updated Sep 26, 2023
2
Explore streaming sequence to Fastq and/or trimFastq steps performance optimizations of run time adn/or cost
#36 opened May 4, 2022 by chrisamiller updated Mar 28, 2023
2
Finish/Verify conversions from CWL documentation Improvements or additions to documentation
#101 opened Mar 23, 2023 by chrisamiller updated Mar 24, 2023 100+
Update hla_consensus.wdl to handle ambiguity codes. enhancement New feature or request
#100 opened Mar 22, 2023 by chrisamiller updated Mar 24, 2023
somatic wgs does not include gnomad filtering enhancement New feature or request
#48 opened May 13, 2022 by chrisamiller updated Mar 24, 2023
1
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