The main aim of this little project is to compare the European allele frequencies of the 1k genomes project with the gnomad frequencies.
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Updated
May 4, 2017 - Python
The main aim of this little project is to compare the European allele frequencies of the 1k genomes project with the gnomad frequencies.
bcftools singularity container
Convert SV VCFs to BED, a wrapper for bcftools query
convert genotype array output into annotated IBD segments
Scripts used on a cluster that demonstrate vcf file manipulation and preparation.
Analysis pipeline for processing paired-end Illumina reads obtained after ancient mtDNA target enrichment capture.
This directory contains material that I've used in different courses
VariantCaller is a wrapper for the 2022 gatk & bcftools best practices + phasing with WhatsHap.
BioC++ Input/Output library
Merge in parallel, speeding up bcftools merge
a tool for quickly getting the correct bcftools command
Here we are going to discuss variant calling on human datasets using GATK Best practices pipeline
Learning the Variant Call Format
Nextflow resequencing pipeline with bwa-mem and freebayes
This script filters false positive alleles from poolseq VCF file created with bcftools.
A Nextflow variant normalization pipeline based on vt and bcftools
A collection of scripts for filtering annotated variant call format files
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