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count variant as biallelic if it's just a non-ref homogeneous site! 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@326 348d0f76-0448-11de-a6fe-93d51630548a
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asivache 2009-04-08 01:57:27 +00:00
parent b49f713336
commit 453d13415d
1 changed files with 8 additions and 2 deletions
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10
java/src/org/broadinstitute/sting/gatk/refdata/rodSAMPileup.java
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@ -112,9 +112,15 @@ public class rodSAMPileup extends ReferenceOrderedDatum implements AllelicVarian
}
if ( observedAlleles.get(0).charAt(0) == refBaseChar && observedAlleles.get(1).charAt(0) == refBaseChar ) varType = NO_VARIANT;
else {
// we know that at least one allele is non-ref;
// if one is ref and the other is non-ref, or if both are non ref but they are the same (i.e.
// homozygous non-ref), we still have 2 allelic variants at the site (e.g. one ref and one nonref)
varType = SNP_VARIANT;
if ( observedAlleles.get(0).charAt(0) == refBaseChar || observedAlleles.get(1).charAt(0) == refBaseChar ) nNonref = 1;
else nNonref = 2;
if ( observedAlleles.get(0).charAt(0) == refBaseChar ||
observedAlleles.get(1).charAt(0) == refBaseChar ||
observedAlleles.get(0) == observedAlleles.get(1)
) nNonref = 1;
else nNonref = 2; // if both observations differ from ref and they are not equal to one another, then we get multiallelic site...
}
}
} catch ( RuntimeException e ) {