SamTools @ BioHPC

SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM aims to be a format that: is flexible enough to store all the alignment information generated by various alignment programs; is simple enough to be easily generated by alignment programs or converted from existing alignment formats; is compact in file size; allows most of operations on the alignment to work on a stream without loading the whole alignment into memory; allows the file to be indexed by genomic position to efficiently retrieve all reads aligning to a locus.

SAMtools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

For more information, please visit the SAMtools home page.

Calculations will be carried out on the BioHPC compute cluster at CBSU. You will receive e-mail notifications when the job is submitted, when it starts, and when it is finished. Output will be available via links embedded in the notification e-mails. For more information about this program and BioHPC interface in general, please visit our Frequently Asked Questions page.

Please acknowledge us in all publications and presentation of work that used our resources using the following text.

You must be a registered user of BioHPC to run SamTools. Please login.

SamTools program:

Input alignment format: BAM SAM

Input alignment file:
No active registered or pipeline files satisfy the selection criteria

view Options:

	Region.
	[-o FILE]. Output file name.
	[-h]. Print header for the SAM output.
	[-H]. Print header only (no alignments).
	[-x]. Output FLAG in HEX (samtools-C specific).
	[-X]. Output FLAG in string (samtools-C specific).
	[-f INT]. Required flag, 0 for unset[0].
	[-F INT]. Filtering flag, 0 for unset[0].
	[-q INT]. Minimum mapping quality [0].
	[-l STR]. Only output reads in library STR [null].
	[-r STR]. Only output reads in read group STR [null].

Cluster: This application can't run at this time - no suitable clusters
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