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23 Open 96 Closed
23 Open 96 Closed
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Issues list

performance: gather of pre refinement vcf is slow
#119 opened May 21, 2024 by Kurt-Hetrick
1
K03A03-1_CONCORDANCE_ON_TARGET_PER_SAMPLE_ARRAY_38.sh
#118 opened May 20, 2024 by Kurt-Hetrick
GRCH37/HG19 PIPELINES: CONCATENATE/COMBINE REJECTED LIFTOVER VARIANTS
#117 opened May 14, 2024 by Kurt-Hetrick
2
do a gt array concordance in a single sge job
#116 opened Apr 30, 2024 by Kurt-Hetrick
switch to doing concordance on grch38 arrays
#115 opened Feb 19, 2024 by Kurt-Hetrick
2
implement vep for grch38 pipelines
#114 opened Jan 10, 2024 by Kurt-Hetrick
validate that samples are not in two different projects in the sample sheet
#113 opened Sep 22, 2023 by Kurt-Hetrick
what if bed files are compressed.
#109 opened Sep 20, 2023 by Kurt-Hetrick
1
qc report prep. single job instead of distributed across cluster.
#107 opened Aug 4, 2023 by Kurt-Hetrick
validate bed files have proper contig names near beginning of submitters
#106 opened Jul 27, 2023 by Kurt-Hetrick
allow for multiple bait, target, titv bed files for non-cmg projects low priority unlikely
#90 opened Oct 26, 2021 by Kurt-Hetrick
1
set a cut-off for number of samples to perform automatic qc report generation enhancement New feature or request
#89 opened Oct 25, 2021 by Kurt-Hetrick
1
switch over to gatk 4 docker/singularity containers
#82 opened Oct 12, 2020 by Kurt-Hetrick
sample count in final vcf
#65 opened Aug 12, 2019 by Kurt-Hetrick
rework cat variants elevated prioritized when time is available
#55 opened Apr 4, 2019 by Kurt-Hetrick
3
add a subfolder in logs with ms prefix low priority unlikely
#50 opened Mar 25, 2019 by Kurt-Hetrick
move qc report prep into a subfolder low priority unlikely
#47 opened Feb 22, 2019 by Kurt-Hetrick
collapse the bed files elevated prioritized when time is available
#42 opened Dec 14, 2018 by Kurt-Hetrick
1
summarize gene summary reports
#22 opened Sep 12, 2018 by Kurt-Hetrick
delete all temp files for a successful run
#21 opened Jul 27, 2018 by Kurt-Hetrick
job arrays
#16 opened Jul 13, 2018 by Kurt-Hetrick
1
handle old sample sheets...and possibly new?
#12 opened Jul 13, 2018 by Kurt-Hetrick
R version for VQSR 2D GMM plots
#8 opened Jul 13, 2018 by Kurt-Hetrick
1
ProTip! Follow long discussions with comments:>50.