update with reference panel stuff

DEploid-dev · Feb 1, 2021 · a89687f · a89687f
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commit a89687f
Showing 1 changed file with 8 additions and 1 deletion.
diff --git a/docs/FAQ.md b/docs/FAQ.md
@@ -33,7 +33,14 @@ To compute the PLAF at each site, we simply take the ratio of *the sum of altern
 
 Since DEploid-BestPractice, we offer new DEploid functionality --- extracting PLAF from the VCF file, enabled by the flag `-plafFromVcf`. It will then extract the Allele Frequency (AF) attribute from the INFO field.
 
-NOTE: To archive a good deconvolution result, prior knowledge of an appropriate PLAF or reference haplotypes are important. I would still recommand to go through the manual computation process when possible. 
+NOTE: To archive a good deconvolution result, prior knowledge of an appropriate PLAF or reference haplotypes are important. I would still recommand to go through the manual computation process when possible.
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+What reference panel should I use?
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+
+1. Definitely use the clonal strains from your own study. Identifying the clonal strains, and inferring their haplotypes would be step one.
+2. Consider to use the clonal strains from the Pf3k or Pf6 dataset as well.
 
 
 Data filtering