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Issues list

Polishing trio-binned assemblies with PEPPER-Margin-DeepVariant
#52 by ASLeonard was closed May 7, 2021
16
No common contigs found between the bam file and the fasta file
#51 by hjaltithorisleifsson was closed Apr 26, 2021
problem when running PEPPER locally
#50 by huangnengCSU was closed May 14, 2021
16
"Critical" errors don't stop the pipeline from continuing
#49 by ASLeonard was closed Apr 22, 2021
1
problems with singularity
#48 by LiShuhang-gif was closed Apr 15, 2021
4
Request for recipe singularty file
#47 by davidecanevazzi was closed May 13, 2021
9
does pepper-margin-deepvariants pipeline support assembly result as the input reference instead of GRCH37 or GRCH38
#46 by huangnengCSU was closed Apr 12, 2021
6
Install from source error
#45 by wjj666 was closed Apr 12, 2021
4
GPU based Singularity container image
#44 by tahashmi was closed Apr 2, 2021
2
Alignment command to reproduce results
#43 by lbal-biomat was closed Apr 2, 2021
5
PacBio HiFi HG002 chr20 results solved This issue is solved and will have official support in the next release.
#42 by tahashmi was closed Apr 1, 2021
12
Problem with singularity
#41 by huangnengCSU was closed Apr 8, 2021
2
Problem with PEPPER Oxford Nanopore variant calling workflow on gpu
#40 by huangnengCSU was closed Mar 20, 2021
3
Any chance of a deepvariant model for bonito-basecalled data?
#39 by oneillkza was closed Mar 4, 2021
1
Substantial loss of sequence when using corrected reads to polish
#38 by ASLeonard was closed Mar 3, 2021
3
Train model for my specific organism
#37 by Irsan88 was closed Mar 2, 2021
2
Question regarding the use of base quality scores
#36 by lbal-biomat was closed Mar 2, 2021
2
Multiallelic SNPs are called as bi-allelic
#35 by naumenko-sa was closed Feb 24, 2021
5
models for viral assembly
#34 by chunlinxiao was closed Feb 19, 2021
1
Cannot locate fasta file
#33 by tomh1lll was closed Jan 25, 2021
2
Problem with Pepper-deepvariant on gpu
#32 by sonaida was closed Mar 5, 2021
4
No luck compiling pepper v0.1 under Anaconda3/2020.07
#31 by ponomarevsy was closed Mar 11, 2021
16
error when parallel deepvariant make_examples
#30 by yingchen69 was closed Jan 6, 2021
3
stalled in RUNNING INFERENCE stage
#29 by lbal-biomat was closed Feb 24, 2021
7
ONNX error while running the test data from quickstart
#28 by yingchen69 was closed Dec 24, 2020
14
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