GROK is “Swiss Army knife” library for processing genomic interval data. GROK operates on genomic regions, annotated chromosomal intervals that represent sequencing short reads, gene locations, ChIP-seq peaks or other genomic features. Applications of GROK include file format conversions, set operations, overlap queries, and filtering and transformation operations. Supported file formats include BAM/SAM, BED, BedGraph, CSV, FASTQ, GFF/GTF, VCF and Wiggle.
:: MORE INFORMATION
IEEE/ACM Trans Comput Biol Bioinform. 2013 Jan-Feb;10(1):200-6. doi: 10.1109/TCBB.2012.170.
Genomic region operation kit for flexible processing of deep sequencing data.
Ovaska K1, Lyly L, Sahu B, J?nne OA, Hautaniemi S.