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
- ANNOVAR
- SnpEff
- WANNOVAR A web server for ANNOVAR.
- biosig tools for variant effect prediction.
Genotype management and GWAS
- plink: a GWAS toolkit
- bedtools & bedops: A toolkit for manipulation of genomic intervals
Linkage
- LINKAGE: single point linkage analysis
- merlin: multi-point linkage analysis
- genehunter: multi-point linkage analysis
Genotype imputation
- impute2
- Eagle
- MACH
- minimac3
- Michigan Imputation Server A web server for fast and efficient imputation and phasing of genotype data.
- TOPMed Imputation Server
R libraries
- Bioconductor: a bioinformatics toolkit written in R
- cran list of Bayesian inference packages.
Fine mapping
- susieR
- FINEMAP
QTL association tools
- Matrix eQTL
- fastqtl
- tensorQTL
LD score regression
- LDSC
- LDpred
TWAS
- TWAS FUSION: a wrapper for a number of TWAS expression prediction methods
Linear mixed model software
- BoltLMM
- fastGWA
- SAIGE