Learning the Variant Call Format
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Updated
Mar 25, 2024 - Perl
Learning the Variant Call Format
Here we are going to discuss variant calling on human datasets using GATK Best practices pipeline
Reusable and maintained Luigi tasks to incorporate in bioinformatics pipelines
BioC++ Input/Output library
Analysis pipeline for processing paired-end Illumina reads obtained after ancient mtDNA target enrichment capture.
A Nextflow variant normalization pipeline based on vt and bcftools
VariantCaller is a wrapper for the 2022 gatk & bcftools best practices + phasing with WhatsHap.
Scripts used on a cluster that demonstrate vcf file manipulation and preparation.
A collection of scripts for filtering annotated variant call format files
This script filters false positive alleles from poolseq VCF file created with bcftools.
convert genotype array output into annotated IBD segments
The main aim of this little project is to compare the European allele frequencies of the 1k genomes project with the gnomad frequencies.
This directory contains material that I've used in different courses
Merge in parallel, speeding up bcftools merge
This repository outlines steps to manage VCF files, including compressing, indexing, querying chromosomes, counting variants, and comparing multiple VCF files using BCFTools.
Convert SV VCFs to BED, a wrapper for bcftools query
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