83 citations
1 runs

samtools fixmate

By Li H., Durbin R., Last update 1494698999
All tools Run this tool

samtools fixmate description

Samtools fixmate fills in mate coordinates, ISIZE and mate related flags from a name-sorted alignment.


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.