✂️ ⚡ Rapid haploid variant calling and core genome alignment
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Updated
Oct 18, 2023 - Perl
✂️ ⚡ Rapid haploid variant calling and core genome alignment
Learning the Variant Call Format
Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
convert your 23andme raw file to VCF | DEPRECATED, please see https://github.com/plantimals/2vcf
Application of pan-genome for population
Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model
Genotyping of segregating mobile elements insertions
microhaplotype visualizer and analyzer
Evolutionary Bioinformatics Toolkit (EBT)
Small scripts for population genetics analysis
Explore and filter structural variant calls from Lumpy and Delly VCF files
Pheno-Ranker is a tool designed for performing semantic similarity analysis on phenotypic data structured in JSON format, such as Beacon v2 Models or Phenopackets v2.
Construct gene haplotype with VCF format files and snpEff annotation.
Checks vcf files and removes loci and samples with too many missings, can also input genotypes in missing (various options for this).
Beacon v2 Reference Implementation (Data ingestion tools) - Actively maintained by the original author
VCF: Variant Call Format files are difficult to understand at first, I already had to dive into them in order to learn how to edit them, so you can use my scripts. Some of these functions already exist in vcftools, but it seems it stopped being updated. so you can use these scripts to do various tasks with them
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