BOL: SAM flags

SAM flags

Poonam Mahapatra — Wed, 29 Jun 2016 15:38:15 -0500

Decoding SAM flags

This utility makes it easy to identify what are the properties of a read based on its SAM flag value, or conversely, to find what the SAM Flag value would be for a given combination of properties.

To decode a given SAM flag value, just enter the number in the field below. The encoded properties will be listed under Summary below, to the right.

Address of the bookmark: https://broadinstitute.github.io/picard/explain-flags.html

Comment by Jit

Jit — Sat, 01 Dec 2018 16:52:14 -0600

Understaning SAMtools

http://www4.ncsu.edu/~rosswhet/BIT815/Overview/Week2/SAMformatAndCLtools.pdf

Comment by Poonam Mahapatra

Poonam Mahapatra — Wed, 29 Jun 2016 15:56:44 -0500

Samtool WIKI

http://davetang.org/wiki/tiki-index.php?page=SAMTools

Comment by Poonam Mahapatra

Poonam Mahapatra — Wed, 29 Jun 2016 15:44:08 -0500

SAM file description https://samtools.github.io/hts-specs/SAMv1.pdf

Comment by Poonam Mahapatra

Poonam Mahapatra — Wed, 29 Jun 2016 15:41:07 -0500

SAM flags https://gist.github.com/davfre/8596159