From d94b3f85bcd56583bc25aa94d9ece3916df39908 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Wed, 20 Mar 2013 20:56:58 -0400 Subject: [PATCH] Increase NUM_BEST_PATHS_PER_KMER_GRAPH in DeBruijnAssembler to 25 -- The value of 11 was too small to properly return a real low-frequency variant in our the 1000G AFR integration test. --- .../gatk/walkers/haplotypecaller/DeBruijnAssembler.java | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/DeBruijnAssembler.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/DeBruijnAssembler.java index f3db422e7..7cf4cc8d3 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/DeBruijnAssembler.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/DeBruijnAssembler.java @@ -78,7 +78,11 @@ public class DeBruijnAssembler extends LocalAssemblyEngine { private final static Logger logger = Logger.getLogger(DeBruijnAssembler.class); private static final int KMER_OVERLAP = 5; // the additional size of a valid chunk of sequence, used to string together k-mers - private static final int NUM_BEST_PATHS_PER_KMER_GRAPH = 11; + + // TODO -- this number is very low, and limits our ability to explore low-frequnecy variants. It should + // TODO -- be increased to a large number of eliminated altogether when moving to the bubble caller where + // TODO -- we are no longer considering a combinatorial number of haplotypes as the number of bubbles increases + private static final int NUM_BEST_PATHS_PER_KMER_GRAPH = 25; public static final byte DEFAULT_MIN_BASE_QUALITY_TO_USE = (byte) 16; private static final int GRAPH_KMER_STEP = 6;