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cio-abcd
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variantinterpretation
Collaborative Interpretation-Pipeline workflow based on nf-core pipeline structure
MIT License
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nfcore template update with restructuring of workflow
#47
sci-kai
opened
1 day ago
0
Missing entries in multi-sample VCF file cause vembrane error
#46
sci-kai
opened
1 day ago
0
Providing vep_cache_version as CLI parameter will be interpreted as integer instead of string
#45
biolancer
opened
1 month ago
0
Support multi-sample VCF files as input
#44
sci-kai
closed
1 day ago
1
Fixed Samtools dict from getSimpleName to getBaseName
#43
sci-kai
closed
1 month ago
0
Samtools dict stops with fasta filenames containg dots
#42
sci-kai
closed
1 month ago
0
Integration of maftools
#41
visuu90
opened
1 month ago
0
HTML report does not show column-summarzing diagrams
#40
sci-kai
opened
5 months ago
0
Always use comma-separated fields to specify multiple values in parameters
#39
sci-kai
opened
5 months ago
0
Change TSV conversion to one-variant-per-row and display one feature on front
#38
sci-kai
opened
5 months ago
0
Automatic bgzip compression
#37
sci-kai
opened
5 months ago
0
Merging of VCF files from the same sample
#36
sci-kai
opened
5 months ago
0
Support for multi-sample VCF files
#35
sci-kai
opened
5 months ago
0
Add example VCF file
#34
sci-kai
opened
8 months ago
0
Release v1.0.0
#33
sci-kai
closed
8 months ago
0
Improve documentation + code and update nf-core template and modules
#32
sci-kai
closed
8 months ago
2
Support running on compressed refgenomes
#31
feiloo
opened
9 months ago
0
Add read_depth as separate parameter for TSV conversion.
#30
sci-kai
closed
9 months ago
0
Add predefined filters
#29
sci-kai
closed
9 months ago
0
change create-vembrane-fields module to have the same header name for allele_fraction
#28
sci-kai
closed
9 months ago
0
Add variant qc
#27
sci-kai
closed
9 months ago
0
TMB module based on vembrane output
#25
biolancer
closed
9 months ago
1
Added python version to create vembrane module for output.
#24
sci-kai
closed
10 months ago
1
Add HTML report
#23
sci-kai
closed
10 months ago
1
Add custom database annotations
#22
sci-kai
opened
11 months ago
0
Add predefined variant filter
#21
sci-kai
closed
9 months ago
0
VCF Preprocessing: Optional prefiltering of Regions-Of-Interest using BED-file
#20
biolancer
opened
1 year ago
0
Add allele fraction and coverage
#19
sci-kai
closed
11 months ago
2
BRCAness SBS3 signature as clinical marker
#18
biolancer
opened
1 year ago
0
Report allele fractions given or calculated from VCF input
#17
sci-kai
closed
11 months ago
1
Extension of the workflow to generate TSV output using vembrane
#16
biolancer
closed
1 year ago
4
set configuration variables for continuous integration
#15
feiloo
closed
10 months ago
2
Lower the errorlevel of the csv.sniffer.has_header heuristic
#14
feiloo
closed
1 year ago
1
Added transcript filtering module based on filter_vep script.
#13
sci-kai
closed
1 year ago
0
Quality control and filtering of input VCF files
#12
sci-kai
closed
9 months ago
1
csv.Sniffer.has_header isnt reliable
#11
feiloo
closed
1 year ago
1
Transcript filter for annotated output
#10
sci-kai
closed
1 year ago
0
TMB calculation module for Tumor-Only-Sequencing
#9
biolancer
opened
1 year ago
7
Add vep annotation module
#8
sci-kai
closed
1 year ago
0
VCF conversion to easily processable format as TSV
#7
sci-kai
closed
1 year ago
1
Report visualization
#6
biolancer
closed
10 months ago
1
Clinically relevant scores
#5
biolancer
opened
1 year ago
1
QC control and coverage visualization
#4
biolancer
opened
1 year ago
2
Incorporation of clinical and methodological metadata
#3
biolancer
opened
1 year ago
0
VCF Preprocessing: Add liftover between reference genomes
#2
sci-kai
opened
1 year ago
0
Set up and configure VEP annotation
#1
sci-kai
closed
1 year ago
2