fixed bad AD in gbs

jendelman · Jan 4, 2024 · 7716174 · 7716174
1 parent 7e471a9
commit 7716174
Showing 1 changed file with 4 additions and 1 deletion.
diff --git a/R/gbs.R b/R/gbs.R
@@ -2,7 +2,9 @@
 #' 
 #' Genotype calls for genotype-by-sequencing (GBS) data
 #' 
-#' VCF input file must contain AD field. Posterior mode and mean genotypes are added as GT and DS fields. GQ is also added based on probability of posterior mode. Binomial calculation uses R/updog package (Gerard et al. 2018) with "norm" prior. Previous INFO is discarded; adds NS, DP.AVG, AF.GT, AB, OD, SE.
+#' VCF input file must contain AD field. Variants with more than 2 alleles are coerced to zero DP, so better to filter them out first.
+#'
+#' Posterior mode and mean genotypes are added as GT and DS fields. GQ is also added based on probability of posterior mode. Binomial calculation uses R/updog package (Gerard et al. 2018) with "norm" prior. Previous INFO is discarded; adds NS, DP.AVG, AF.GT, AB, OD, SE.
 #' 
 #' @param in.file VCF input file
 #' @param out.file VCF output file
@@ -64,6 +66,7 @@ gbs <- function(in.file, out.file, ploidy, bias=TRUE, n.core=1,
     if (any(is.na(alt)))
       alt[is.na(alt)] <- 0
 
+    AD <- apply(cbind(ref,alt),1,paste,collapse=",")
     DP <- ref+alt
     DP.AVG <- paste("DP.AVG",round(mean(DP),1),sep="=")