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Alterations to scripts for better performance. Grid search now expands the sens/spec tradeoff (90 was far too aggressive against hapmap chr20), and 20 max gaussians was too many, and caused errors. For consensus genotypes: remember to gunzip the beagle outputs before converting to VCF. Also, beagle can in fact create 'null' alleles in certain circumstances. I'm not sure what exactly those circumstances are, but those sites should be ignored. When it does, all alleles apear to be set to null, so this should not affect the actual phasing in the output VCF.

This commit is contained in:
Christopher Hartl 2012-01-20 23:07:59 -05:00
parent f3564bbf43
commit 9b4f6afa21
1 changed files with 5 additions and 0 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
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@ -241,6 +241,11 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
String alleleA = beagleGenotypePairs.get(0);
String alleleB = beagleGenotypePairs.get(1);
if ( alleleA.equals("null") || alleleB.equals("null") ) {
logger.warn("Beagle produced 'null' alleles at location "+ref.getLocus().toString()+". Ignoring.");
return 0;
}
// Beagle always produces genotype strings based on the strings we input in the likelihood file.
String refString = vc_input.getReference().getDisplayString();
if (refString.length() == 0) // ref was null