Minimum Depth of Coverage in Stacks2

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Yi-Cheng Tseng

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Sep 11, 2021, 8:10:43 AM9/11/21

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Hi all,

I am currently using ref_map.pl for "Reference Mapping".

The pstacks in stacks ver. 1.48, there is an option "-m" for "minimum depth of coverage to report a stack".

Is there any option for filtering "depth of coverage", similar to that of "-m" in pstacks, in stacks2 for reference mapping?

Best,

YiCheng

Catchen, Julian

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Sep 20, 2021, 5:36:40 PM9/20/21

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Hi YiCheng,

In general, no, there is not a specific flag to limit loci based on depth of coverage. Stacks2 relies on the SNP caller to call sites as heterozygous or homozygous and if there are not enough reads to do so, sites will not have a statistically significant call and will not be included in the analysis. You can require additional reads to make a call statistically significant by decreasing the alpha value for the SNP calling model in gstacks (say from the default of 0.05 to 0.01).