How does gstacks discard alignments?

[rosed...@gmail.com]

Hello Stacks Community,
In the paper, Population genomics analysis with RAD, reprised: STACKS 2, it is stated that after running ref_map, "...users should check for the fractions of alignments discarded due to low mapping quality..." I checked my gstacks log report and found a number of "primary alignments with insufficient mapping quality." I am wondering how this number is determined.

What criteria/threshold does gstacks use to decide if an alignment is of low or insufficient mapping quality?

Thanks for any help you can provide,
Jen

[Catchen, Julian]

Hi Jen,

 

The gstacks program reads the mapping quality score assigned by the aligner (MAPQ). The default value for this is a phred score of 10 but can be controlled with the --min-mapq flag to gstacks.

 

Best,

 

julian

[rosed...@gmail.com]

Thank you!