Programs

PLINK

• whole genome association analysis toolset
• does a lot of different things: data management, summary statistics for quality control, population stratification detection, basic association testing, multimarker predictors, haplotypic tests, copy number variant analysis, etc.
• More details on website

SAMTOOLS

• Utilities for manipulating alignments in the SAM, BAM, CRAM format: includes sorting, merging, indexing, generating alignments in a per-position format
• samtools pileup -v inputfile.bam -> generates a vcf
• samtools phase -> call and phase heterozygous SNPs
• samtools bam2fq -> converts bam into FASTQ file formats

BCFTOOLS

• set of utilities that manipulate variant calls in the vcf and bcf files
• convert 23andme into VCF: bcftools convert -c ID,CHROM,POS,AA -s SampleName -f 23andme-ref. fa –tsv2vcf 23andme.txt -0z -o out.vcf.gz

VCFTOOLS

• tools for vcf and bcf files mainly to summarize data, run calculations on data, filter out data, and convert data into other useful file formats

TABIX/bgzip

• TABIX indexes tab-delimited genome position file and creates an index file
• input file needs to be position sorted and compressed by bgzip