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search_file_by_column

simple utility for indexing and retrieving lines based on the value of a column

sift4g

Sorting Intolerant From Tolerant For Genomes

sigprofilerextractor

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.

snpviewer

A program for visualising Affymetrix SNP array data

spliceai

A deep learning-based tool to identify splice variants

splicedistance

VEP plugin to annotate distance to the nearest splice junction

taad_analysis

Scripts and modules utilised for analysing the data referred to in <some-paper>

taad_summarizer

tabix

Note: tabix and bgzip binaries are now part of the HTSlib project.

translatedna

Quickly translate DNA in chosen frame and optionally line up translation and DNA sequence. Designed for convenience and simplicity.

updio

updiva

Detect Uniparental Disomy from VCF data

vase

Variant Annotation, Segregation and Exclusion for family or cohort based rare-disease sequencing studies.

vase_family_filtering_workflow

vcf_concat_mixed

Concatanate tabix indexed and sorted VCFs for the same samples the same contig may appear in multiiple VCFs

vcfhacks

simple to use commandline programs for VCF filtering and manipulation

vep_plugins

Plugins for the Ensembl Variant Effect Predictor (VEP)

wait_for_process

Simple utility to wait for matching running processes to finish and exit.

watchfilesize

Utility for monitoring the size of files on the commandline