From 32be212484e790701b226c92f9fe9c2bb46e8e4c Mon Sep 17 00:00:00 2001 From: Lucas Czech Date: Tue, 24 Sep 2024 12:34:36 +0200 Subject: [PATCH] Add FST doc about missing data --- doc/md/fst.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/md/fst.md b/doc/md/fst.md index f04fa98..db5bea1 100644 --- a/doc/md/fst.md +++ b/doc/md/fst.md @@ -18,7 +18,7 @@ We recommend to use one of our two estimators, as they are correctly accounting Our recommendation is to use the Hudson estimator with a cutoff for low frequencies (either via `--filter-total-snp-min-count` or `--filter-total-snp-min-frequency`), see for instance [10.1101/gr.154831.113](https://doi.org/10.1101/gr.154831.113) for a rationale. -The values per window are computed using the window averaging as described [here](../wiki/Windowing#window-averaging-policy), in order to scale the results per base pair. +The values per window are computed using the window averaging as described [here](../wiki/Windowing#window-averaging-policy), in order to scale the results per base pair. Note that by default, no filtering is applied to the data. That includes missing positions - we leave it open to the user to decide how they want to deal with those (i.e., which exact filter settings are fitting for their purposes). Without any filtering however, this can lead to an inflation of negative values of FST, see [here](https://github.com/lczech/grenedalf/issues/32). We hence recommend to apply some form of numerical filter when missing data is present.