nikostourvas acorn_poolseq_pipeline issues

nikostourvas / acorn_poolseq_pipeline

0 stars 0 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

VarScan filter ignores -min-coverage argument

#23 nikostourvas opened 12 months ago
0
bam_filtering.sh outputs tmp files inside script directory

#21 nikostourvas opened 1 year ago
0
Add filter for p-value in VCF filtering SNP output

#19 nikostourvas closed 1 year ago
2
Improve VarScan efficiency

#18 nikostourvas opened 1 year ago
0
Avoid producing raw SAM files

#17 nikostourvas closed 1 year ago
0
VarScan call variants in different regions of the genome

#16 nikostourvas closed 12 months ago
1
Using VarScan mpileup2cns uses the same p-value for SNPs and INDELs

#15 nikostourvas closed 1 year ago
0
grenedalf fails to convert VarScan filtered VCF to sync file

#14 nikostourvas closed 12 months ago
1
Use of temporary directories

#13 nikostourvas closed 12 months ago
1
The pipeline expects a data directory inside the project's directory.

#12 nikostourvas closed 1 year ago
1
MultiQC only reports results for the last sample filtered with Trimmomatic

#11 nikostourvas opened 1 year ago
0
GAPIT fail to install

#10 nikostourvas closed 1 year ago
0
Pipeline continues even if individual scripts produce error codes

#9 nikostourvas closed 1 year ago
0
Extract allele frequencies from poolseq data

#8 nikostourvas closed 1 year ago
1
add check for raw file integrity

#7 nikostourvas closed 1 year ago
1
bam-readcount does not count depth in markduplicate BAM files correctly

#6 nikostourvas closed 12 months ago
1
MultiQC report

#5 nikostourvas closed 1 year ago
1
Set 'singularity' branch as default

#4 nikostourvas closed 1 year ago
0
Add pipeline steps for analyzing regular WGRS samples which will be used to validate pool-seq results

#3 nikostourvas closed 12 months ago
0
Add variable in the pipeline script to globally control number of cpu threads used by each software

#2 nikostourvas closed 12 months ago
0
New version of VarScan released

#1 nikostourvas closed 1 year ago
0