Utilities / Statistics for BAM


Given a BAM file and an index file (.bai) for it, this tool counts how many alignments there are per each chromosome.




Please note that in addition to BAM file you have to provide an index file. You can create the index file using the tool "Index BAM".


Output is a table (bam-stats.tsv) listing the chromosomes, their lengths, and how many reads align to each chromosome.


This tool is based on the SAMtools package. Please cite the article The Sequence alignment/map (SAM) format and SAMtools by Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) Bioinformatics, 25, 2078-9. [PMID: 19505943].