aryarm varCA issues - Githubissues

aryarm / varCA

Use an ensemble of variant callers to call variants from ATAC-seq data

MIT License

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issues

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mamba

#52 portbo opened 1 year ago
0
Error in rule predict

#51 silentFUSU closed 1 year ago
0
ERROR conda.core.link:_execute(730)

#47 xuanxuan-Jin opened 2 years ago
0
Exit (1) error when running pipeline using example data.

#46 rm1238 opened 2 years ago
2
handle vardict iupac ambiguity codes

#44 aryarm closed 2 years ago
0
add GT info to the VCFs

#43 shinlin77 opened 2 years ago
11
VarDict-java produces malformed VCF

#42 aryarm closed 2 years ago
5
handling a scATAC custom reference genome from 10x

#41 aryarm opened 2 years ago
2
Not all of the samples requested have provided input

#40 umasstr opened 3 years ago
6
warn or error gracefully if index files don't exist

#39 aryarm opened 3 years ago
0
Error: "An output file is marked as pipe, but consuming jobs are part of conflicting groups."

#38 Rubbert opened 3 years ago
11
Single-end support

#37 Rubbert opened 3 years ago
2
add citation info

#36 aryarm closed 3 years ago
0
comply with snakemake standards

#35 aryarm opened 3 years ago
0
create contributing guidelines

#34 aryarm closed 3 years ago
0
a smaller test dataset

#33 aryarm opened 3 years ago
0
explicit channel specifications

#32 aryarm closed 3 years ago
0
remove non-zero exit code from 2vcf.py snakemake rule

#31 aryarm closed 3 years ago
0
prepare.yml environment yields conflicts with strict channel_priority

#30 aryarm opened 3 years ago
2
make channel specifications in environment files explicit

#29 aryarm closed 3 years ago
0
2vcf.py exits with a non-zero exit code when executed by snakemake

#28 aryarm closed 3 years ago
3
update install instructions

#27 aryarm opened 3 years ago
0
handle varscan iupac ambiguity codes

#26 aryarm closed 3 years ago
0
Varscan generates a REF allele that is not compatible with GATK.

#25 lindenb closed 3 years ago
4
Vardict error.

#24 lindenb opened 3 years ago
1
ChildIOException: File/directory is a child to another output:

#23 lindenb closed 3 years ago
2
Classification model for mouse?

#22 YiweiNiu closed 3 years ago
2
excessive memory usage when predicting variants

#21 aryarm opened 4 years ago
2
ldpaths error when using prepare.yaml conda env

#20 aryarm opened 4 years ago
1
only install the necessary variant caller dependencies

#19 aryarm opened 4 years ago
1
snakemake validation

#18 aryarm opened 4 years ago
1
skip rmdups and peak calling steps if input is BAM

#17 aryarm closed 4 years ago
0
convert final pipeline output to vcf

#16 aryarm closed 4 years ago
0
create a snakemake file for running both pipelines all at once

#15 aryarm closed 4 years ago
0
run the post-processing steps in the prepare pipeline in parallel

#14 aryarm opened 4 years ago
0
write a script for calculating the following stats on each atac seq cell line

#13 aryarm closed 4 years ago
0
change sge mode in strelka config script

#12 aryarm closed 4 years ago
0
add genotypes (GT field) to final vcf

#11 aryarm closed 2 years ago
1
update dependencies and freeze them

#10 aryarm closed 4 years ago
3
example data

#9 aryarm closed 4 years ago
3
docker

#8 aryarm closed 4 years ago
7
output figures in a snakemake report

#7 aryarm opened 4 years ago
0
output in VCF format

#6 aryarm closed 4 years ago
2
create READMEs for the snakemake pipelines

#5 aryarm closed 4 years ago
0
combine this repo with the merge_callers repo

#1 aryarm closed 5 years ago
0
don't use gatk selectvariants + allow varca to output SNVs and indels in the same VCF

#2 aryarm opened 5 years ago
1
varscan precision recall curve

#3 aryarm closed 5 years ago
3
making manta and strelka less picky

#4 aryarm closed 4 years ago
1