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sanger-tol
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variantcalling
This Nextflow DSL2 pipeline calls variants on long read alignment. It is run after sanger-tol/readmapping in the Sanger ToL production suite but with options to run on unaligned reads.
https://pipelines.tol.sanger.ac.uk/variantcalling
MIT License
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Samtools view
#85
muffato
closed
3 days ago
3
Missing align flag
#84
muffato
closed
3 days ago
3
Assess nf-core/phylonetwork
#83
muffato
opened
1 week ago
0
Variant density
#82
muffato
opened
2 weeks ago
0
Define test datasets for population genomics
#81
muffato
opened
2 weeks ago
3
Assess Popgen48/scalepopgen
#80
muffato
opened
2 weeks ago
0
Assess nf-core/sarek
#79
muffato
opened
2 weeks ago
3
Fixed the bug in the filtering of multiple PacBio files
#78
gq1
closed
1 month ago
3
Fix when multiple PacBio files are given
#77
gq1
closed
1 month ago
0
Increase CPU and memory for CI because default Github runner resource doubled
#76
gq1
closed
1 month ago
9
Compress the .pi output
#75
muffato
opened
2 months ago
0
Bug fix release 1.1.2
#74
gq1
closed
3 months ago
1
Wrong fai channel name
#73
gq1
closed
3 months ago
2
No such variable: ch_index
#72
muffato
closed
3 months ago
0
Index VCF file
#71
gq1
opened
4 months ago
0
Bug fix fasta for release
#70
gq1
closed
4 months ago
1
Bug fix fasta
#69
gq1
closed
4 months ago
2
Pipeline finishes without running DeepVariant when fasta file named with .fa not .fasta
#68
gq1
closed
4 months ago
0
Release1.1.0 - dev
#67
gq1
closed
6 months ago
3
Release 1.1.0 to main branch
#66
gq1
closed
6 months ago
3
Population genomics
#65
muffato
opened
6 months ago
1
Runs of Homozygosity
#64
muffato
opened
6 months ago
1
Pacbio align
#63
gq1
closed
6 months ago
8
VCFTOOLs site_pi and het options
#62
gq1
closed
7 months ago
4
Patch samtools/sort to add reference input
#61
gq1
opened
7 months ago
0
Per site nucleotide diversity
#60
priyanka-surana
closed
7 months ago
2
Remove input read indices, make reference index optional and combine same sample together
#59
gq1
closed
7 months ago
4
Template and module updating
#58
gq1
closed
9 months ago
8
New tolsoft details
#57
muffato
closed
10 months ago
3
Dummy PR to test the fix_linting workflow
#56
muffato
closed
10 months ago
4
Update sanger_test_full.yml -test linting fixing
#55
gq1
closed
10 months ago
3
Use the tolsoft access token to fix linting
#54
muffato
closed
10 months ago
1
Tower action version updating 2
#53
gq1
closed
10 months ago
7
Use the latest version of the Tower action
#52
muffato
closed
10 months ago
1
Our new convention is use per-pipeline directories under pipeline_info/
#51
muffato
closed
10 months ago
2
Updated CI
#50
muffato
closed
10 months ago
3
Calculate allele frequency
#49
priyanka-surana
opened
11 months ago
0
Add optional read mapping subworkflow
#48
priyanka-surana
closed
6 months ago
0
Structural variation
#47
priyanka-surana
opened
1 year ago
0
Variant calling with short read data
#46
priyanka-surana
opened
1 year ago
3
Optional readmapping subworkflow
#45
priyanka-surana
closed
11 months ago
1
Combine multiple libraries from the same sample
#44
priyanka-surana
closed
7 months ago
1
Create indices
#43
priyanka-surana
closed
7 months ago
1
Heterozygous sites across genome
#42
priyanka-surana
opened
1 year ago
1
Calculate InDel size distribution
#41
priyanka-surana
opened
1 year ago
0
Create flag for homozygous alternatives
#40
priyanka-surana
opened
1 year ago
0
Add calculation for heterozygosity
#39
priyanka-surana
closed
7 months ago
1
Merging main into dev after release
#38
priyanka-surana
closed
1 year ago
1
Add doi after first release
#37
priyanka-surana
closed
1 year ago
1
Release 1.0.0
#36
priyanka-surana
closed
1 year ago
1
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