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

View the Project on GitHub broadinstitute/picard

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

Find SAM flag by property:

To find out what the SAM flag value would be for a given combination of properties, tick the boxes for those that you'd like to include. The flag value will be shown in the SAM Flag field above.