bcftools

There are 0 repository under bcftools topic.

• davetang / learning_vcf_file

  Learning the Variant Call Format

  vcfvcftoolsbcftoolsvcf-formatmulti-sample-vcfvcf-filescall-variantsgatk
  Language:Perl 136

• digo4 / Clinical-Genomics

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

  bcftoolsbowtie2bwa-memcutadaptfastpfastqcfreebayesgatk-bestpracticesgatk-cnvgatk-joint-variant-calling-workflowgatk4gatk4-haplotypecallerpicardsamtoolstrimgaloretrimmomaticvarscan
  Language:Shell 13

• PavlidisLab / bioluigi

  Reusable and maintained Luigi tasks to incorporate in bioinformatics pipelines

  luigi-taskbioinformaticsbcftoolsvcfannogatkslurmensembl-vep
  Language:Python 9

• biocpp / biocpp-io

  BioC++ Input/Output library

  biocppfastafastqfastq-formatbcfbcftoolsbiopythoncplusplus-20fasta-formatheader-onlymodern-cppseqansequence-analysisvcfvcf-formatcsvinput-outputtsvc-plus-plus
  Language:C++ 8

• mnievesc / Ancient_mtDNA_Pipeline

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

  ancient-dna-sequencesbam-filesbcftoolsbwafastq-filesfastqcmtdnapipelinesamtools
  Language:Shell 7

• TRON-Bioinformatics / tronflow-vcf-postprocessing

  A Nextflow variant normalization pipeline based on vt and bcftools

  bcftoolsbioinformaticsnextflownormalizing-variantstronflowvcfvt
  Language:Shell 6

• RhettRautsaw / VariantCaller

  VariantCaller is a wrapper for the 2022 gatk & bcftools best practices + phasing with WhatsHap.

  bcftoolsgatkgatk-bestpracticesindelsphasingsamtoolssnpsvariant-calling
  Language:Python 4

• sdhutchins / vcf-prepping

  Scripts used on a cluster that demonstrate vcf file manipulation and preparation.

  vcfbcftoolswhole-genome-sequencingwgsexome-sequencing
  Language:Shell 3

• AnstMikh / DNA

  pipeline: from sra, bed, vcf to plink

  samtoolsbcftoolsplinkplink2sratoolkitangsdpipelinepythonrhapmap
  Language:Jupyter Notebook 2

• openb-io / ibd-pipeline

  convert genotype array output into annotated IBD segments

  geneticsibdbeaglevcfbcftoolsibd-pipeline23andmeancestrydna
  Language:Shell 2

• scholl-lab / vcf-filtering

  A collection of scripts for filtering annotated variant call format files

  bcftoolsgeneticskidney-diseaserare-diseaserare-variant-analysissnpeffvcfsnpsift
  Language:Shell 2

• yenon118 / VisualVariants

  The goal of this project is to create a R package and executable scripts to visualize variants in Variant Call Format (VCF) files and Bcftools processed tab-delimited files.

  rvcfbcftools
  Language:R 2

• 1tilly / wgs-exercise

  The main aim of this little project is to compare the European allele frequencies of the 1k genomes project with the gnomad frequencies.

  bioinformaticsbcftoolsvcf-files1000genomespython3python
  Language:Python 1

• biodata-fun / course_material

  This directory contains material that I've used in different courses

  genomicsnextflow-pipelinesvariant-callingtutorialbcftoolsfreebayes
  1

• 0-Ioniel-0 / guppy_MR

  Repository for scripts used to estimate guppy (Poecilia reticulata) mutation rate.

  bambcftoolsdenovogatk4gvcfmutation-ratepythonsamtoolsvcf
  Language:Python 0

• adrianodemarino / bcftools_merge_parallel

  Merge in parallel, speeding up bcftools merge

  genetic-algorithmparallel-computingbcftoolsmergebcftools-mergevcf-files
  Language:Shell 0

• CHRUdeLille / bcftools_containers

  bcftools singularity container

  bcftoolshtslibnext-generation-sequencingngssingularitysingularity-containerssingularity-hubvcfvcftools
  Language:Shell 0

• gibsonMatt / bioneer

  a tool for quickly getting the correct bcftools command

  bcftoolsbioinformaticsllmpythondynamic-few-shot
  Language:Python 0

• maurya-anand / liftover

  Convert genomic coordinates from the Human Genome version 19 (hg19) to version 38 (hg38)

  bcftoolsgenomicsliftovervariant-call-formatvariant-calling
  Language:Python 0

• nicolo-tellini / S.cerevisiaeData

  1,674 S.cerevisiae genomics data

  bcftoolscerevisaegvcfbwagenomicsbioinformaticsdatadata-scienceopensource
  Language:Shell 0

• cnr-ibba / nf-resequencing-mem

  Nextflow resequencing pipeline with bwa-mem and freebayes

  nextflow-pipelineresequencingbwa-memfreebayesnextflownextflow-dsl2bcftools
  Language:Nextflow

• dantaki / sv2bed

  Convert SV VCFs to BED, a wrapper for bcftools query

  vcfstructural-variationbcftoolshtslib
  Language:Python

• Grelot / reserveBenefit--snpsdata_analysis

  Codes i wrote for the paper "genomic resources for Mediterranean fishes"

  reservebenefitradseqgenomesnpbashrvcftoolsbedtoolssamtoolsbwa-mempython3bcftoolscontainersingularityhtslib
  Language:Shell