BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. ## I never used it EMBOSS is a free Open Source software analysis package specially developed for the needs of […]

Variant Annotation Tools and Tools for Genomic Variants processing VCFtools is a “program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF […]

This post is my own “repository” of useful linux commands, which I (or SirShurf) have found, changed and used. You can take them, you can ask questions, I will try to answer. Renaming files in directory This example replaces “vcf.gz.recode” by “SNP” for f in *.vcf; do echo “$f”; a=”$(echo […]