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Issues: snakemake-workflows/dna-seq-gatk-variant-calling

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17 Open 9 Closed
17 Open 9 Closed
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Issues list

Help with dna-seq-gatk-variant-calling
#42 opened Oct 25, 2023 by Sahu-Mousumi
TypeError in calling.smk rule merge_variants. The bwa mapping stops after creating the indexes files.
#39 opened Jun 5, 2023 by ClaraApicella
1
7
rule plot_stats fails with "OverflowError: value too large to convert to npy_uint32"
#36 opened Aug 19, 2022 by gernophil
4
VQSR not fully implemented
#35 opened Jul 18, 2022 by lczech
4
REMOVE_DUPLICATES is false according to logs in rule mark_duplicates
#34 opened Jun 19, 2022 by gernophil
can't set java opts for rule recalibrate_base_qualities
#33 opened Jun 18, 2022 by gernophil
Choice of reference genome
#32 opened Feb 14, 2022 by ThibauldMichel
2
missing python dependency in rule plot_stats
#31 opened Oct 21, 2021 by pmginacio
2
Errors in two rules terminating run
#30 opened Aug 13, 2021 by CAllex-Buckner
2
Not executed fastqc for specified inputs
#27 opened Jun 21, 2020 by nkimoto
1
Running without known-variants
#21 opened Feb 28, 2020 by silastittes
3
Failed to open environment file
#19 opened Dec 14, 2019 by CharlesJB
Which singularity image is used?
#18 opened Dec 11, 2019 by ManavalanG
1
Direct output to directory of interest
#17 opened Nov 21, 2019 by ManavalanG
1
snpeff with custom genome database
#13 opened Sep 12, 2019 by RvV1979
README report link served through RawGit will stop working
#12 opened Aug 9, 2019 by corburn
Output vcf.gz instead of vcf.
#9 opened May 31, 2019 by johanneskoester
ProTip! Follow long discussions with comments:>50.