diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/PickSequenomProbes.java b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/PickSequenomProbes.java index 0f08239ff..57de80817 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/PickSequenomProbes.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/PickSequenomProbes.java @@ -33,9 +33,13 @@ public class PickSequenomProbes extends RefWalker { public void initialize() { if ( SNP_MASK != null ) { logger.info("Loading SNP mask... "); - ReferenceOrderedData snp_mask = new ReferenceOrderedData("snp_mask", - new java.io.File(SNP_MASK), TabularROD.class); - + ReferenceOrderedData snp_mask; + if ( SNP_MASK.contains("dbsnp")) { + snp_mask = new ReferenceOrderedData("snp_mask",new java.io.File(SNP_MASK),rodDbSNP.class); + } else { + snp_mask = new ReferenceOrderedData("snp_mask", + new java.io.File(SNP_MASK), TabularROD.class); + } snpMaskIterator = snp_mask.iterator(); } }