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21 Open 44 Closed
21 Open 44 Closed
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Issues list

Use store_object_as_json to store parameters standardization
#180 opened Aug 12, 2024 by nwiltsie
GATK Trio mode best-practices
#178 opened Aug 3, 2024 by yashpatel6
@yashpatel6
GATK v4.6.0.0
#176 opened Jul 1, 2024 by yashpatel6
@yashpatel6
Use methods.setup_process_afterscript() for process logs
#172 opened Jun 10, 2024 by nwiltsie
@yashpatel6
docker-gatk name update
#164 opened May 7, 2024 by yashpatel6
GATK v3.7.0 Docker image update name
#163 opened May 7, 2024 by yashpatel6
Update VQSR commands to follow recent GATK best practices
#133 opened Jun 1, 2023 by tyamaguchi-ucla
Compress raw VCFs
#124 opened Feb 25, 2023 by yashpatel6
Contamination file extension
#117 opened Dec 20, 2022 by yashpatel6
Error: Invalid parameter type for parameter input_csv
#111 opened Nov 5, 2022 by alkaZeltser
1
Process multi_sample_wgs:recalibrate_base:run_ApplyBQSR_GATK (30) terminated with an error exit status (3)
#103 opened Aug 25, 2022 by graceooh
@yashpatel6
2
Process single_sample_wgs:run_HaplotypeCallerGVCF_GATK (30) terminated with an error exit status (1)
#99 opened Jul 15, 2022 by raagagrawal
2
Move dev test files - call-gSNP - @yashpatel6
#98 opened Jul 13, 2022 by yashpatel6
@yashpatel6
scatter_count > 50
#73 opened Mar 19, 2022 by RoniHaas
5
Update VCF filtration and QC
#68 opened Mar 9, 2022 by yashpatel6
@yashpatel6
Review the Perl filtering script enhancement New feature or request
#67 opened Mar 5, 2022 by yashpatel6
@yashpatel6
Registered dataset input/methods
#59 opened Feb 4, 2022 by yashpatel6
@yashpatel6
Error paired_sample_wgs:reheader_interval_bams
#50 opened Jan 5, 2022 by tgebo
@yashpatel6
2
Errorpaired_sample_wgs:remove_realigned_bams
#49 opened Jan 5, 2022 by tgebo
Use singleID instead of normalID when there is only one sample from a patient enhancement New feature or request
#17 opened Sep 1, 2021 by shutaojccc
1
Update Dockerfile for SNV filtering script
#8 opened Aug 13, 2021 by yashpatel6
@yashpatel6
ProTip! no:milestone will show everything without a milestone.