alipirani88 / snpkit

Modular workflow for Microbial Variant Calling and SNP diagnostics.

https://alipirani88.github.io/snpkit/

alipirani88/snpkit Issues

Reference genome file requirements
Closed 3 months ago2
Update snpkit config files to reflect reference database location change to turbo from nfs.
Closed 4 months ago
nucmer.error - critical files could not be used.
Updated 4 months ago
Add downsampling step as a default.
Closed 4 months ago1
Rewrite gubbins_env.yml file
Closed 4 months ago1
Add gubbins and mask argument to phase 2 step 3
Closed 4 months ago
/bin/sh: vcf-consensus: command not found
Closed 4 years ago
remove old results from core_temp_dir. the workflow uses the outdated results in case one of the steps fails.
Closed 4 months ago
ImportError: No module named pandas
Closed 4 years ago
Extract positions filtered by Indel Proximate filters and assign N instead of reference allele
Closed 4 years ago1
error generating snpEff config file.
Closed 4 years ago1
add seqtk to environment
Closed 4 years ago
fix documentation label of genome size option
Closed 4 years ago1
Move creation and check of Sequence Dictionary using Picard and other index generating steps to the initial part of pipeline.
Closed 4 years ago
Error: More than 3 Locus Tags were found at - Indel matrix step exits if there are more than 3 locus tags in variant annotation
Closed 4 years ago
write checks in second step of the pipeline - if any vcf file is empty indicating if a step failed in variant calling.
Closed 4 years ago1
fix conda activate statement for -gubbins yes
Closed 4 years ago
add pyfasta to environment
Closed 4 years ago
add cyvcf2 to environment
Closed 4 years ago
add memory profiler to environment
Closed 4 years ago
add biopython to environment
Closed 4 years ago
ImportError: No module named cyvcf2
Closed 4 years ago
include pyfasta module in environment.yml file
Closed 4 years ago1
remove trailing underscore from the end of sample names
Closed 4 months ago
create a more simple/generalizable example config file
Closed 4 months ago
Remove the need to update binbase: path in config file and autiomatically search the installed executables.
Closed 4 years ago
add documentation using only gubbins + iqtree
Closed 4 months ago
When a SNV is present in multiple genes (in this case 3 genes), only 2 locus tags/strand info are listed and not 3 -- here: CD630_18440, CD630_18560, CD630_18550
Closed 4 years ago1
SNP mat and Indel mat .csv --> .tsv
Closed 4 years ago
Remove gene symbol and insert Locus Tag in field 4
Closed 4 years ago2
Indel row name issue?
Closed 4 years ago1
I/O performance issues
Closed 5 years ago1
Feature Addition: Outgroup option
Closed 4 years ago
low fq AND low mq in code matrix
Closed 4 months ago1
Resolving Branch length issues specific to outgroup inclusion.
Closed 4 years ago
Generate non-gubbins tree; run Raxml and Iqtree on pre-gubbins filtered alignment.
Closed 4 months ago1
Integrating variant QC script into the pipeline.
Closed 4 years ago10
Generates a wrong prefix if the alignment fasta file path has "." character. script name: gubbins_iqtree_raxml.sh
Closed 5 years ago
Downsample coverage to 100X: generate a test data from high coverage datasets
Closed 5 years ago1
Add an optional outgroup flag/option into the gubbins job generating script.
Closed 5 years ago3
Incorporate outgroup inclusion in analysis.
Closed 5 years ago1
Variant QC folder results
Closed 4 years ago
variant matrix strand/coding/non-coding bug
Closed 4 years ago43
move beast module
Closed 5 years ago
Brief Read me type file for each iteration of the pipeline run
Closed 5 years ago1
Final Results folder directory sctructure
Closed 5 years ago
unmask phage variants in variant matrix code files
Closed 4 months ago2
variant matrix code numbers
Closed 4 months ago4
naming of pre- and post- gubbins files
Closed 5 years ago
Variant Calling Pipeline Bugs/Feature
Closed 6 years ago