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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.
This commit is contained in:
Mark DePristo 2013-03-20 20:56:58 -04:00
parent 6d7d21ca47
commit d94b3f85bc
1 changed files with 5 additions and 1 deletions
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6
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/DeBruijnAssembler.java
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@ -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;