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Issues list

No common contigs found between the bam file and the fasta file
#51 by hjaltithorisleifsson was closed Apr 26, 2021
PL issue
#142 by kishwarshafin was closed Apr 21, 2022
run error on run_deepvariant.py
#162 by windforclouds was closed Aug 16, 2022
not producing PEPPER_HP_OUTPUT_2.vcf.gz output for sample data pepper polishing (v.04)
#177 by plnspineda was closed Mar 14, 2023
generated haplotagged BAM file
#206 by nikhita-damaraju was closed Apr 25, 2024
Is the model using in create consensus reads same as call variant?
#18 by YanJiunLiu was closed Nov 10, 2020
1
PEPPER_variant_calling pipeline in shell scripts instead of docker?
#20 by yingchen69 was closed Nov 23, 2020
1
Bat genome optimal parameters
#26 by desmodus1984 was closed Jan 12, 2021
1
models for viral assembly
#34 by chunlinxiao was closed Feb 19, 2021
1
Any chance of a deepvariant model for bonito-basecalled data?
#39 by oneillkza was closed Mar 4, 2021
1
"Critical" errors don't stop the pipeline from continuing
#49 by ASLeonard was closed Apr 22, 2021
1
nanopore genome calling questions
#59 by RichardCorbett was closed May 17, 2021
1
For the phased results in the vcf file
#73 by Yechao94 was closed Jun 15, 2021
1
OSError: Unable to open file (truncated file: eof = 96, sblock->base_addr = 0, stored_eof = 2048)
#81 by siupenyau was closed Aug 1, 2021
1
Polishing with short reads
#83 by wchow was closed Aug 12, 2021
1
present of overlay in my filesystem
#85 by zhoudreames was closed Aug 26, 2021
1
precisionFDA Truth Challenge V2 - link broken
#87 by tararickman was closed Aug 18, 2021
1
Support cis index for large genomes
#102 by kishwarshafin was closed Sep 23, 2021
1
guppy 5 hac model
#106 by rrazaghi was closed Oct 21, 2021
1
Intermediate bam size
#108 by ghost was closed Oct 28, 2021
1
Multiple bams
#122 by myonaung was closed Jan 10, 2022
1
Problems about “UserWarning”
#126 by LiShuhang-gif was closed Jan 18, 2022
1
Bacteria
#128 by joergFLI was closed Jan 31, 2022
1
Support for Conda / local without admin rights
#132 by tuannguyen8390 was closed Feb 15, 2022
1
Quick question about Deep Learning and Varian Calling
#146 by ghost was closed May 26, 2022
1
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