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By Li H., Durbin R., Last update 1494698999
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bamcheck description

Bamcheck collects statistics from BAM files. The output can be visualized using plot-bamcheck.

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.