A list of commonly used software tools around the lab

Next generation sequencing

  • fastqc: A quality control tool for high throughput sequence data.
  • BWA: alignment & mapping sequences against reference genome
  • samtools: manipulation and variant calling for sequence alignment in BAM format
  • GATK: Variant calling tool for sequence alignment data in BAM format
  • picard: manipulating high-throughput sequencing data and formats
  • vcftools: manipulation of VCF files
  • bcftools: a faster replacement of vcftools, and also provides variant calling function
  • tabix: index and query for tab delimited genomic position files
  • IGV: visualization tool for interactive exploration of sequence alignment data

Variant annotation

Genotype management and GWAS

  • plink: a GWAS toolkit
  • bedtools & bedops: A toolkit for manipulation of genomic intervals


  • LINKAGE: single point linkage analysis
  • merlin: multi-point linkage analysis
  • genehunter: multi-point linkage analysis

Genotype imputation

R libraries

Fine mapping

  • susieR

QTL association tools

  • Matrix eQTL
  • fastqtl
  • tensorQTL

LD score regression

  • LDSC
  • LDpred


  • TWAS FUSION: a wrapper for a number of TWAS expression prediction methods

Linear mixed model software

  • BoltLMM
  • fastGWA