Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / kishwarshafin/pepper issues and pull requests

#210 - Runtime on CCS reads

Issue - State: open - Opened by Lionward 3 months ago - 1 comment

#209 - required "-m/--model_path"

Issue - State: open - Opened by KANGYUlab 3 months ago

#208 - PEPPER-Margin-DeepVariant takes more cores than limit

Issue - State: open - Opened by martabaragli 8 months ago - 1 comment

#207 - Error in margin phase :No valid VCF entries found!

Issue - State: open - Opened by kch4221 8 months ago

#206 - generated haplotagged BAM file

Issue - State: closed - Opened by nikhita-damaraju 10 months ago

#205 - Issue with docker GPU

Issue - State: open - Opened by martabaragli 10 months ago

#204 - phasing between R9 and R10 data

Issue - State: open - Opened by Yijun-Tian 11 months ago

#203 - Can pepper be used for short contigs?

Issue - State: open - Opened by zhan4429 about 1 year ago

#202 - Samples w/older guppy

Issue - State: open - Opened by dmjask about 1 year ago

#201 - Install local copy of pepper.

Pull Request - State: closed - Opened by TheSequencingCenter about 1 year ago - 1 comment

#200 - Do I have to train a model for specific organism ?

Issue - State: open - Opened by Modernism-01 about 1 year ago

#199 - Snp prediction accuracy is low in all difficult mapping areas

Issue - State: open - Opened by oranges7 about 1 year ago - 1 comment

#198 - Joint Genotyping Recommendation

Issue - State: open - Opened by SophieS9 about 1 year ago

#197 - Fix transformer model output shape error

Pull Request - State: open - Opened by AyanoClarke over 1 year ago

#196 - ImportError with Singularity

Issue - State: open - Opened by aCoalBall over 1 year ago

#195 - Root privileges

Issue - State: open - Opened by Meer9234 over 1 year ago

#194 - MARGIN using param file for older model

Issue - State: open - Opened by thainsCEB over 1 year ago

#193 - Model for Guppy 6.5.7 SUP and/or Dorado 0.34

Issue - State: open - Opened by gchevignon over 1 year ago - 1 comment

#192 - Dockerfile

Issue - State: open - Opened by yneuma over 1 year ago

#191 - Bump torch from 1.10.0 to 1.13.1

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#190 - HiFi_variant_calling tutorial inconsistent

Issue - State: open - Opened by splaisan over 1 year ago

#189 - resuming the run

Issue - State: open - Opened by Shruti-BioCode over 1 year ago - 1 comment

#188 - Could not read from reference fasta file.

Issue - State: closed - Opened by sinha-shruti over 1 year ago - 1 comment

#187 - Issues while trying use the singularity image

Issue - State: open - Opened by kiratalreja3 over 1 year ago

#186 - Deepvariant pepper settings for duplex calling

Issue - State: open - Opened by alvinwt almost 2 years ago

#184 - Installation issue with pytorch

Issue - State: open - Opened by noncodo almost 2 years ago - 1 comment

#183 - am I running this wrong?

Issue - State: open - Opened by shinlin77 almost 2 years ago - 7 comments

#182 - Can you make pepper available on conda, please?

Issue - State: open - Opened by yuukiiwa almost 2 years ago - 1 comment

#181 - g.vcf

Issue - State: closed - Opened by shinlin77 almost 2 years ago - 1 comment

#180 - Calloc issue with docker even after allocating memory - margin polish

Issue - State: closed - Opened by sofiabanu almost 2 years ago - 1 comment

#179 - Local PEPPER installation for variant calling

Issue - State: closed - Opened by leonorpalmeira almost 2 years ago - 4 comments

#178 - Disabling dawnsampling in pepper_margin_deepvariant ?

Issue - State: open - Opened by kiflu-23 almost 2 years ago - 4 comments

#176 - Seq2Seq_atn.py

Issue - State: closed - Opened by ElaheAghapour about 2 years ago - 1 comment

#175 - ./. GQ=0 in gvcf where I have high coverage as homozygous reference

Issue - State: closed - Opened by aguygarner about 2 years ago - 1 comment

#173 - issue in running Pepper

Issue - State: closed - Opened by tahashmi over 2 years ago - 1 comment

#172 - Phasing into a single phaseset across targeted region of interest

Issue - State: closed - Opened by smf96 over 2 years ago - 6 comments

#171 - Critical Vulnerabilities in the published Docker image

Issue - State: closed - Opened by rberg2 over 2 years ago - 2 comments

#170 - pysam not working

Issue - State: closed - Opened by Az513 over 2 years ago - 1 comment

#169 - .csi indexing when phasing

Issue - State: closed - Opened by aguygarner over 2 years ago - 4 comments

#168 - ERROR: basic_string::substr

Issue - State: closed - Opened by chilampoon over 2 years ago - 4 comments

#167 - Ambiguous IUPAC bases appearing in output VCF violate VCF Spec

Issue - State: open - Opened by rickymagner over 2 years ago - 4 comments
Labels: bug, wontfix

#166 - Depth differences between r0.5 and r0.8

Issue - State: closed - Opened by VLeducq over 2 years ago - 3 comments

#165 - Genotype quality graph always 0

Issue - State: open - Opened by cdebuck over 2 years ago - 1 comment
Labels: bug

#164 - optimal GPU type

Issue - State: closed - Opened by paracontias over 2 years ago - 1 comment

#163 - Setting Guppy version

Issue - State: closed - Opened by vladimirsouza over 2 years ago - 5 comments

#162 - run error on run_deepvariant.py

Issue - State: closed - Opened by windforclouds over 2 years ago

#161 - Margin-[E::hts_open_format] Failed to open file .bam

Issue - State: closed - Opened by infotmatician over 2 years ago - 3 comments

#160 - RefCall vs. PASS

Issue - State: closed - Opened by yifeng-evo over 2 years ago - 3 comments

#159 - ImportError

Issue - State: closed - Opened by BrendaLee1 over 2 years ago - 1 comment

#158 - Model training data

Issue - State: closed - Opened by mproberts99 over 2 years ago - 2 comments

#157 - No valid VCF entries found!

Issue - State: closed - Opened by infotmatician over 2 years ago - 4 comments

#156 - AD field looks wierd

Issue - State: closed - Opened by Yijun-Tian over 2 years ago - 5 comments

#155 - PEPPER standalone

Issue - State: closed - Opened by myonaung over 2 years ago - 2 comments

#154 - Bump numpy from 1.21.0 to 1.22.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#153 - undefined symbol: libdeflate_free_compressor

Issue - State: closed - Opened by liuzhen51032 over 2 years ago - 3 comments

#152 - Further output description

Issue - State: closed - Opened by nsanchezcollantes over 2 years ago - 2 comments

#151 - version of margin in latest docker image

Issue - State: closed - Opened by splaisan over 2 years ago - 1 comment

#150 - How to run margin in HiFi analysis?

Issue - State: closed - Opened by splaisan over 2 years ago - 1 comment

#149 - Training margin

Issue - State: closed - Opened by luskry over 2 years ago - 1 comment

#148 - Running into AttributeError

Issue - State: closed - Opened by sagnikbanerjee15 over 2 years ago - 3 comments

#146 - Quick question about Deep Learning and Varian Calling

Issue - State: closed - Opened by daniusparres over 2 years ago - 1 comment

#145 - Is there a way to collect more information in the reported .g.vcf?

Issue - State: closed - Opened by RichardCorbett over 2 years ago - 2 comments

#144 - Running PEPPER_DEEPVARIANT pipeline on aarch64

Issue - State: closed - Opened by CaptainYvel almost 3 years ago - 5 comments

#143 - PEPPER hifi model training problems

Issue - State: closed - Opened by jessieshen97 almost 3 years ago - 8 comments

#142 - PL issue

Issue - State: closed - Opened by kishwarshafin almost 3 years ago

#141 - Problem with make_image module

Issue - State: closed - Opened by daniusparres almost 3 years ago - 3 comments

#140 - Can I use deep-trio in the pepper-margin-deepvariant pipeline?

Issue - State: closed - Opened by jessieshen97 almost 3 years ago - 3 comments

#139 - Can PEPPER deal with CLR sequencing data?

Issue - State: closed - Opened by LiShuhang-gif almost 3 years ago - 2 comments

#138 - Bump numpy from 1.16.6 to 1.21.0

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago - 1 comment
Labels: dependencies

#137 - variants are not called by run_pepper_margin_deepvariant

Issue - State: closed - Opened by Josephhungyi almost 3 years ago - 9 comments

#136 - polish_assembly deprecated? How to get two haplotype assembly files?

Issue - State: closed - Opened by dithiii almost 3 years ago - 2 comments

#135 - polish with different haplotype fasta

Issue - State: closed - Opened by zmz1988 almost 3 years ago - 7 comments

#134 - sm_86 support in r0.7-gpu docker

Issue - State: closed - Opened by fellen31 almost 3 years ago - 2 comments

#133 - cannot locate bam file

Issue - State: closed - Opened by zhaotao1987 almost 3 years ago - 5 comments

#132 - Support for Conda / local without admin rights

Issue - State: closed - Opened by tuannguyen8390 almost 3 years ago - 1 comment

#131 - Stitch module error

Issue - State: closed - Opened by reachsagaya almost 3 years ago - 8 comments

#130 - Specific chromosome run

Issue - State: closed - Opened by tahashmi about 3 years ago - 11 comments

#129 - Candidate detection in PEPPER-SNP

Issue - State: closed - Opened by GuillaumeHolley about 3 years ago - 4 comments

#128 - Bacteria

Issue - State: closed - Opened by joergFLI about 3 years ago - 1 comment

#127 - typo in your installation instructions

Issue - State: closed - Opened by rainwala about 3 years ago - 2 comments

#126 - Problems about “UserWarning”

Issue - State: closed - Opened by LiShuhang-gif about 3 years ago - 1 comment

#125 - Many unphased variants in amplicon data

Issue - State: closed - Opened by AJTDaedalus about 3 years ago - 9 comments

#124 - What base type does ./. （in vcffile output）indicate？

Issue - State: closed - Opened by lxxiaoxiaLi about 3 years ago - 7 comments

#123 - Training questions

Issue - State: closed - Opened by GuillaumeHolley about 3 years ago - 11 comments

#122 - Multiple bams

Issue - State: closed - Opened by myonaung about 3 years ago - 1 comment

#121 - Pepper SNP training fails on DGX1 server

Issue - State: closed - Opened by GuillaumeHolley about 3 years ago - 2 comments

#120 - Bring in updates made in DV v1.3.0

Issue - State: closed - Opened by SHuang-Broad about 3 years ago - 2 comments

#119 - Can PEPPER-Margin-DeepVariant used in nanopore RNA-seq?

Issue - State: closed - Opened by chilampoon about 3 years ago - 3 comments

#118 - r0.7 for Guppy4 data

Issue - State: closed - Opened by aquaskyline about 3 years ago - 7 comments

#117 - explanation on intermediate files

Issue - State: closed - Opened by myonaung about 3 years ago - 5 comments

#116 - error No valid VCF entries found after PEPPER SNP calling

Issue - State: closed - Opened by myonaung about 3 years ago - 4 comments

#115 - error messages for incomplete deepvariant-run on HPC.

Issue - State: closed - Opened by myonaung about 3 years ago - 7 comments

#114 - How to obtain TRUTN_BAM_H1 and TRUTH_BAM_H2.

Issue - State: closed - Opened by minghuaxu about 3 years ago - 2 comments

#113 - prefix

Issue - State: closed - Opened by husamia about 3 years ago - 2 comments

#112 - r0.6 seems stuck

Issue - State: closed - Opened by GuillaumeHolley about 3 years ago - 25 comments

#111 - If other BAMs are in output folder, `run_pepper_margin_deepvariant` fails.

Issue - State: closed - Opened by williamrowell about 3 years ago - 4 comments