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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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Documatation
#35
gq1
closed
1 year ago
3
Splitting input reference file
#34
gq1
closed
1 year ago
2
Logo and copyright update
#33
muffato
closed
1 year ago
2
to make sure csi index file can be used for input bam file
#32
gq1
closed
1 year ago
1
Filtering deepvariant
#31
gq1
closed
1 year ago
2
Update sample sheet format, and checking script, add two test data
#30
gq1
closed
1 year ago
2
update github workflow in template
#29
gq1
closed
1 year ago
1
Template
#28
gq1
closed
1 year ago
1
Template
#27
gq1
closed
1 year ago
2
add one level for the output dir
#26
gq1
closed
1 year ago
0
Automate input normalisation
#25
muffato
closed
1 year ago
0
Documentation part 1
#24
priyanka-surana
closed
2 years ago
2
Automate input
#23
priyanka-surana
closed
2 years ago
4
README
#22
priyanka-surana
closed
1 year ago
0
Addition of contribution
#21
DLBPointon
closed
2 years ago
0
Adding gatk4
#20
DLBPointon
closed
2 years ago
0
Module: Add GATK4
#19
DLBPointon
closed
1 year ago
0
Large test: `Meles meles`
#18
priyanka-surana
closed
1 year ago
0
Medium test: `Erithacus rubecula`
#17
priyanka-surana
closed
1 year ago
0
Small test: `Asterias rubens`
#16
priyanka-surana
closed
1 year ago
0
Nf-core module: samtools_view
#15
priyanka-surana
closed
2 years ago
0
Local module: automate_io
#14
priyanka-surana
closed
2 years ago
0
Script: automate_input_output.sh
#13
priyanka-surana
closed
2 years ago
0
Local module: samplesheet_check
#12
priyanka-surana
closed
2 years ago
0
Script: samplesheet.py
#11
priyanka-surana
closed
2 years ago
0
Subworkflow: Check input
#10
priyanka-surana
closed
2 years ago
0
Local module: input_check
#9
priyanka-surana
closed
2 years ago
0
Unit test dataset
#8
priyanka-surana
closed
2 years ago
0
Add SAMTOOLS stats prior to GATK4
#7
DLBPointon
closed
1 year ago
0
Moving data to S3
#6
DLBPointon
closed
1 year ago
1
merge adding_picard_cm (now GATK4)
#5
DLBPointon
closed
2 years ago
1
Linting compatibility
#4
DLBPointon
closed
2 years ago
0
Addition of an Illumina_VC sub-workflow
#3
DLBPointon
closed
1 year ago
2
Adding test
#2
DLBPointon
closed
2 years ago
0
Addition of test data and samplesheet.csv
#1
DLBPointon
closed
2 years ago
0
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