bedtools - the swiss army knife for genome arithmetic
The main features of arq5x/bedtools2 are: File Utilities.
Open-source alternatives to arq5x/bedtools2 include: andersenlab/bam-toolbox — A bam toolbox. brentp/mosdepth — fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing. brentp/somalier — fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy". brentp/vcfanno — annotate a VCF with other VCFs/BEDs/tabixed files. daler/gffutils — GFF and GTF file manipulation and interconversion. darwinawardwinner/mergesam — Automate common sam & bam conversions.
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
