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Issues list

Bacteria
#128 by joergFLI was closed Jan 31, 2022
1
typo in your installation instructions
#127 by rainwala was closed Mar 16, 2022
2
Problems about “UserWarning”
#126 by LiShuhang-gif was closed Jan 18, 2022
1
Many unphased variants in amplicon data
#125 by AJTDaedalus was closed Jan 31, 2022
9
What base type does ./. （in vcffile output）indicate？
#124 by lxxiaoxiaLi was closed Jan 18, 2022
7
Training questions
#123 by GuillaumeHolley was closed Jan 24, 2022
11
Multiple bams
#122 by myonaung was closed Jan 10, 2022
1
Pepper SNP training fails on DGX1 server
#121 by GuillaumeHolley was closed Jan 10, 2022
2
Bring in updates made in DV v1.3.0
#120 by SHuang-Broad was closed Mar 16, 2022
2
Can PEPPER-Margin-DeepVariant used in nanopore RNA-seq?
#119 by chilampoon was closed Jan 10, 2022
3
r0.7 for Guppy4 data
#118 by aquaskyline was closed May 15, 2022
7
explanation on intermediate files
#117 by myonaung was closed Dec 21, 2021
5
error No valid VCF entries found after PEPPER SNP calling
#116 by myonaung was closed Dec 16, 2021
4
error messages for incomplete deepvariant-run on HPC.
#115 by myonaung was closed Dec 15, 2021
7
How to obtain TRUTN_BAM_H1 and TRUTH_BAM_H2.
#114 by minghuaxu was closed Dec 9, 2021
2
prefix
#113 by husamia was closed Dec 21, 2021
2
r0.6 seems stuck
#112 by GuillaumeHolley was closed Jan 5, 2022
25
If other BAMs are in output folder, run_pepper_margin_deepvariant fails.
#111 by williamrowell was closed Nov 22, 2021
4
Bug in pepper_deepvariant:r0.6 docker run_pepper_margin_deepvariant.py
#110 by jdemeul was closed Nov 5, 2021
4
Getting GVCF after variant_call completed
#109 by GuillaumeHolley was closed Nov 2, 2021
2
Intermediate bam size
#108 by ghost was closed Oct 28, 2021
1
Follow up on #101
#107 by SHuang-Broad was closed Nov 3, 2021
8
guppy 5 hac model
#106 by rrazaghi was closed Oct 21, 2021
1
Optional step - getting haplotagged BAM and phased VCF
#105 by ghost was closed Oct 14, 2021
6
HG002 dataset
#104 by GuillaumeHolley was closed Oct 25, 2021
9
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