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Gleeson-Lab
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wxs_pipeline
Starting with BAMs and FASTQs, follow GATK 4.0 Best Practices up to generating a joint-genotyped VCF
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Update Snakefile
#21
chchuk
closed
9 months ago
0
Update Snakefile
#20
chchuk
closed
9 months ago
0
Update repository path variable
#19
brcopeland
opened
2 years ago
2
Replace bwa with bwa-mem2
#18
brcopeland
opened
2 years ago
0
Adjust Walltimes Based on Size of Data
#17
brcopeland
opened
2 years ago
2
bed file as an input in Amplicon mode
#16
chchuk
closed
2 years ago
0
Disable PCR Duplicates Marking for Amplicon Sequencing
#15
brcopeland
closed
2 years ago
3
FixMateInformation (Picard)
#14
JiaweiShen1116
opened
2 years ago
4
Variant Annotation
#13
brcopeland
opened
2 years ago
3
HaplotypeCaller is running with the check_contamination.done file
#12
brcopeland
opened
2 years ago
2
Adjust VQSR if Given a Small amount of Data
#11
brcopeland
opened
2 years ago
0
Add single-sample variant calling
#10
brcopeland
closed
2 years ago
7
Adjust Calling Intervals Based on Size of Input Files
#9
brcopeland
opened
2 years ago
2
Implement Unit Testing with snakemake
#8
brcopeland
opened
2 years ago
0
Change BED File for WES
#7
brcopeland
opened
2 years ago
3
Implement Archival of Final Data
#6
brcopeland
opened
2 years ago
8
Additional QC Tests?
#5
brcopeland
opened
2 years ago
4
Implement Sex Typing
#4
brcopeland
opened
2 years ago
6
Implement Downloading/Creating all Reference Data Files
#3
brcopeland
closed
2 years ago
3
Implement Confirming Relatedness when a PED file is provided
#2
brcopeland
closed
2 years ago
1
Update Documentation
#1
brcopeland
closed
2 years ago
3