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Reducing the size of the reference padding in the HaplotypeCaller.

This commit is contained in:
Ryan Poplin 2013-02-17 11:09:00 -05:00
parent 029de71a44
commit b7e9c342c7
1 changed files with 1 additions and 1 deletions
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protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
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@ -270,7 +270,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
private CachingIndexedFastaSequenceFile referenceReader;
// reference base padding size
private static final int REFERENCE_PADDING = 900;
private static final int REFERENCE_PADDING = 400;
// bases with quality less than or equal to this value are trimmed off the tails of the reads
private static final byte MIN_TAIL_QUALITY = 20;