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Issues: Kurt-Hetrick/CIDR_SOMATIC_WES_PIPELINES

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42 Open 28 Closed
42 Open 28 Closed
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Issues list

run somatic vcf metrics on coding/titv bed file
#70 opened Sep 6, 2024 by Kurt-Hetrick
CALCULATE BARCODE SUMMARY METRICS
#69 opened Jul 23, 2024 by Kurt-Hetrick
2
investigate haplotype caller gvcf contamination allele fraction cut-off
#68 opened Jul 19, 2024 by Kurt-Hetrick
generate cidrseqsuite samplesheet from paired samplesheet in paired calling pipeline
#67 opened Jul 19, 2024 by Kurt-Hetrick
bug/feature enhancement to qc report generated solely on sample sheet
#66 opened Jul 17, 2024 by Kurt-Hetrick
combine barcode metrics output per flow cell
#64 opened Jun 28, 2024 by Kurt-Hetrick
dynamically set computational resources request based on how many lanes are in cidr samplesheet
#60 opened Jun 11, 2024 by Kurt-Hetrick
bugs in grch37 qc pipeline
#58 opened Apr 29, 2024 by Kurt-Hetrick
investigate end tasks execution
#56 opened Feb 12, 2024 by Kurt-Hetrick
add mate flags/run samblaster for umi workflow?
#55 opened Jan 30, 2024 by Kurt-Hetrick
reconfigure mutect2 calls/filtering
#53 opened Jan 18, 2024 by Kurt-Hetrick
benchmark tumor only vs tumor/normal calls
#52 opened Jan 18, 2024 by Kurt-Hetrick
submission notification. how many lanes were submitted
#50 opened Jan 4, 2024 by Kurt-Hetrick
evaluate gatk 4.5.0.0
#48 opened Dec 14, 2023 by Kurt-Hetrick
LIMITATION: initial paired calling pipeline
#42 opened Oct 18, 2023 by Kurt-Hetrick
validate that there are no somatic variants from the normal in mutect2 output vcf metrics
#41 opened Oct 16, 2023 by Kurt-Hetrick
validate that bed files exist
#39 opened Sep 7, 2023 by Kurt-Hetrick
CollectVariantCallingMetrics bed files. 1 or 0 based.
#38 opened Aug 25, 2023 by Kurt-Hetrick
1
there should only be one unique bed files per type (bait, target, etc) in input manifest
#37 opened Aug 24, 2023 by Kurt-Hetrick
bed files will need to be in predetermined location as of right now
#35 opened Aug 17, 2023 by Kurt-Hetrick
1
collapse all bed files before calling
#31 opened Apr 18, 2023 by Kurt-Hetrick
remove mito chrom from aneuploidy check report
#28 opened Mar 3, 2023 by Kurt-Hetrick
fix header in per chromosome verifybamid report
#27 opened Mar 3, 2023 by Kurt-Hetrick
mutect filter output statistics
#26 opened Mar 2, 2023 by Kurt-Hetrick
mutect2 vcf output
#25 opened Mar 2, 2023 by Kurt-Hetrick
1
ProTip! Updated in the last three days: updated:>2024-11-29.