Sickle in Africa

R version 4.1.2 with data.table, qqman, rehh, SeqArray, IsoRelate, moimix, BiocManager, RColorBrewer

Dysgu (v1.8.7) structural variant calling with samtools and bcftools v1.23

Trim Galore v0.6.10 with fastqc v0.12.1, cutadapt v5.2, multiqc v1.33, pandoc v3.1.3, TexLive 3.1

REGENIE GWAS

KING relatedness tool with R v4.1.2 (r-base-core) for generating IBD plots on the fly

EIGENSOFT for population genetics analysis

gkmSVM and deltaSVM tools by Dongwon Lee and the Beer Lab

minimac4 (v4.1.6) with savvy (v2.1.0) genomics tools

BEAGLE v5.2 genetic data phasing and imputation

vcflib for manipulating VCF files

MetaMinimac2 and aggRSquare by Yu et al for meta-imputation

coalNN allele age estimate by the Palamara Lab

ngs tools: bwa (v0.7.18), bwa-mem2, samtools (v1.20), htslib (v1.20)

program for genome coordinates conversion between different assemblies (v0.6.4)

PLINK1.9 and PLINK2 population genetics tools by Shaun Purcell and Christopher Chang

Affymetrix Analysis Power Tools

ILLUMINA DRAGMAP software with htslib

Illumina GenCall algorithm. Execute using: iaap-cli gencall -h Also contains bcftools +gtc2vcf

selscan v2.0.0

The executable is DMLE+2.2