From 5c0099df90478e9dc0e84c2637201d428d4f745f Mon Sep 17 00:00:00 2001 From: Sebastian Schoenherr Date: Tue, 22 Jan 2019 16:47:33 +0100 Subject: [PATCH] Set minimal coverage to 5 (same as in mtDNA-Server) --- src/main/java/genepi/mut/util/VariantCaller.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/main/java/genepi/mut/util/VariantCaller.java b/src/main/java/genepi/mut/util/VariantCaller.java index 69ac5eb..6bfe406 100644 --- a/src/main/java/genepi/mut/util/VariantCaller.java +++ b/src/main/java/genepi/mut/util/VariantCaller.java @@ -170,12 +170,12 @@ public static double calcLevelTop(VariantLine line) { } private static boolean checkAlleleCoverage(VariantLine line, double minorPercentFWD, double minorPercentREV) { - if (line.getTopBasePercentsREV() * line.getCovREV() < 3 - || (line.getTopBasePercentsFWD() * line.getCovFWD()) < 3) { + if (line.getTopBasePercentsREV() * line.getCovREV() <= 5 + || (line.getTopBasePercentsFWD() * line.getCovFWD()) <= 5) { return false; } - if ((minorPercentREV * line.getCovREV() < 3) || (line.getTopBasePercentsFWD() * line.getCovFWD()) < 3) { + if ((minorPercentREV * line.getCovREV() <= 5) || (line.getTopBasePercentsFWD() * line.getCovFWD()) <= 5) { return false; }