Utilities / Convert SAM to BAM, sort and index


Given a SAM file, this tool converts it to BAM, sorts it and creates an index file (.bai).




This tool is similar to the preprocessing tool which you are prompted to use when importing SAM files to Chipster. The preprocessing tool is based on the (pickier) Picard package and runs on your own computer, while this one is based on the more relaxed SAMtools package and runs on the server.


Output is a sorted BAM file and an index file.


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].