GooglingTheCancerGenome sv-callers issues

GooglingTheCancerGenome / sv-callers

Snakemake-based workflow for detecting structural variants in genomic data

https://research-software.nl/software/sv-callers

Apache License 2.0

77 stars 35 forks source link

issues

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Error in running analysis.yml

#82 poddarharsh15 closed 11 months ago
1
Sample entry question for germline anlaysis

#81 mxiong2 closed 1 year ago
1
ModuleNotFoundError in line 7 of /home/mai/sv-callers/workflow/Snakefile

#80 mxiong2 closed 1 year ago
1
bwa-mem2 compatibility

#79 Avramis closed 1 year ago
1
Workflow fails to run due to recent incompatibility of dependencies

#78 arnikz closed 1 year ago
0
VCF final outputs

#77 mtinti closed 1 year ago
1
Incorrect named wildcards reported in s/p modes

#76 arnikz closed 2 years ago
0
Integrate viola-sv into post-processing step

#75 arnikz closed 2 years ago
0
Copy Number Calling

#74 azhark2 closed 2 years ago
1
Incorrect sample wildcard(s) returned in delly rule

#73 arnikz closed 2 years ago
0
Incorrect sample wildcard(s) returned in survivor rules

#72 arnikz closed 2 years ago
0
Use GitHub Container Registry instead of Docker Hub

#71 arnikz closed 2 years ago
0
compile error

#70 trinidadmartin closed 3 years ago
12
Updating GRIDSS to a newer version

#69 lsantuari closed 1 year ago
4
Missing SV type parameter in DELLY filtering

#68 jbreynier closed 2 years ago
4
Enable sv-callers in the workflow catalog

#67 arnikz closed 2 years ago
0
Java heap space error while running GRIDSS

#66 lsantuari closed 1 year ago
2
Error in rule delly_p using paired-sample SV calling

#65 ccastane9 closed 2 years ago
2
Compatibility for bwa-mem2 indexed fasta files

#64 arumds closed 2 years ago
1
bwa-mem2 + multisample sv-calling and genotyping on non-human genomes

#63 arumds closed 1 year ago
1
empty output

#62 xiaojingshi closed 3 years ago
10
manta seems to be written for python 2.7

#61 pierrj closed 3 years ago
1
What is the principle of merging records from multiple callers?

#60 yangyxt closed 3 years ago
2
Run this pipeline on PBS based HPC

#59 yangyxt closed 1 year ago
1
gridss error while running with sv-callers

#58 nitha26 closed 3 years ago
2
Processing trios for de novo mutations

#57 lsantuari closed 2 years ago
1
Add a Codacy badge to README.md

#56 codacy-badger closed 3 years ago
0
Use GitHub Actions instead of Travis CI

#55 arnikz closed 2 years ago
0
all.vcf file produced by SURVIVOR merge cannot be read by SVA

#54 lsantuari closed 1 year ago
1
HPC Usage issue on slurm ?

#53 Navin-techi closed 2 years ago
8
HPC cluster usage

#52 nitha26 closed 4 years ago
2
GermlineSV Final Genotype Merged callsets

#51 nitha26 closed 4 years ago
2
GermlineSV_calling in WGS (centos7 local machine)

#50 nitha26 closed 4 years ago
6
Speed up conda install

#49 arnikz closed 4 years ago
1
LSF cluster usage

#48 TnakaNY closed 1 year ago
4
sv-callers Installation in local machine and input files

#47 nitha26 closed 4 years ago
14
CI testing fails because of timeout

#46 arnikz closed 4 years ago
0
Add bc to environment.yaml

#45 annawoodard closed 4 years ago
0
MAX_HEAP calculation fails if `bc` is not available

#44 annawoodard closed 4 years ago
3
Generate FASTA index files if not provided

#43 arnikz opened 4 years ago
0
Validate input BAM file(s) prior SV calling

#42 arnikz opened 4 years ago
0
Update test data for the workflow

#41 arnikz closed 4 years ago
18
Job submission fails via Xenon CLI on Slurm v19

#40 lsantuari closed 4 years ago
3
Add CHANGELOG.md file

#39 arnikz closed 4 years ago
0
Enable comments in sample.csv file

#38 arnikz closed 4 years ago
0
Use new docker images for CI testing

#37 arnikz closed 4 years ago
0
Update README & pin down software versions

#36 arnikz closed 4 years ago
0
Update SV callers to the latest versions

#35 arnikz opened 4 years ago
2
Validate workflow config in YAML

#34 arnikz closed 4 years ago
1
Fix IO error handing

#33 arnikz closed 4 years ago
0