Explain SAM Flags (original) (raw)

Picard

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

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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.

SAM Flag:

Toggle first in pair / second in pair