Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html

Learning the Variant Call Format

Here we are going to discuss variant calling on human datasets using GATK Best practices pipeline

Partial reimplementation of bcftools for VCF Zarr

A Nextflow pipeline for NGS variant calling on SARS-CoV-2. From FASTQ files to normalized and annotated VCF files from GATK, BCFtools, LoFreq and iVar.

Analysis pipeline for processing paired-end Illumina reads obtained after ancient mtDNA target enrichment capture.

[WORK IN PROGRESS]: Pysam2 is a module for Python 3.6 or newer for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib v2 C-API, the same one that powers samtools, bcftools, and tabix.

Reusable and maintained Luigi tasks to incorporate in bioinformatics pipelines

BioC++ Input/Output library

Tools to unpack Bruker Esprit (.bcf) data files. This will not work on compressed or encrypted files.

A Nextflow variant normalization pipeline based on vt and bcftools

Experimental bcftools port to support BCF2; DEPRECATED by htslib and htsbox

bcftools snp calling pipeline for SLURM

A collection of scripts for filtering annotated variant call format files

calculates tajima's D from bcftools query input

supervised machine learning to filter a VCF generated using BCFTools

Filter and select variant consequence annotations from snpEff, VEP or bcftools

No description available

GWAS analysis using alignemnt tools bwa/bowtie2 and variant calling with samtools/bcftools and association analysis with PLINK/GWAStools.

Docker container for bcftools

Maintenance scripts used with the htslib/samtools/bcftools repositories

Lightly modified versions of htslib and bcftools to merge VCF streams.

outsider-module: 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.

Script to convert the GP column of a VCF to minor allele dosage. Assumes column AF (alternate allele frequency). Requires bcftools.

Convert Genbank to GFF compatible with "bcftools csq"

benchmark of Samtools/Bcftools, GATK and VariantTools

WDL workflows for patched bcftools with GCS resilience fixes