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Old 12-05-2012, 03:55 AM   #15
Location: Boston, MA

Join Date: Apr 2010
Posts: 36

Originally Posted by iansealy View Post
The GATK Unified Genotyper can do this too. Check the --output_mode option on It sounds like you want EMIT_ALL_CONFIDENT_SITES or EMIT_ALL_SITES.

As can freebayes. By default it outputs all sites of even extremely low confidence, P(site polymorphic | data) >= 0.0001 (parameter -P --pvar).

The intent is that users filter their results downstream, and also that it be almost impossible to run the program and get no output due to default filtering options. Generally, this provides more flexibility than filtering the site prior to reporting, but it does produce copious amounts of output.

I found this thread because samtools is refusing to produce output in a (simulated) case where both freebayes and the gatk work just fine without any tweaks...
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