Nheyer's repositories
bcftools
This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib
Comparative-Annotation-Toolkit
tools only
FixOverlapVCF
A tool to fix the funky format tags produced by bcftools
freebayes
Bayesian haplotype-based genetic polymorphism discovery and genotyping.
genomics_scripts
scripts produced to work with the notch2nl regions
hal
Hierarchical Alignment Format
htslib
C library for high-throughput sequencing data formats
jumpcutter
Automatically edits vidx. Explanation here: https://www.youtube.com/watch?v=DQ8orIurGxw
linkage_calc
A C++ program that utilizes gametic linkage disequilibrium, permutation tests, and bootstrapping to calculate linkage from a multi-sample gvcf
odgi
optimized dynamic genome graph implementation
phast
PHAST
sequenceTubeMap
displays multiple genomic sequences in the form of a tube map
SUMSTATS
Format of data for GWAS summary statistics