samtools idxstats description
Samtools idxstats retrieves and print stats in the index file. The output is TAB delimited with each line consisting of reference sequence name, sequence length, # mapped reads and # unmapped reads.
Parent program: samtools
SAMTools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. It is very convinient for handling reads mapped to reference genome. Normally SAMtools is used in intermediate step between raw read mapping and SNP or variants callingm, because it allows to effeciently store mapped reads.