Problem replacing contigs in a dbsnp vcf using Picard SortVcf

[idedios]

Right now I'm trying to change the contigs in the dbsnp vcf to match those of my reference genome (from 1, 2, ..., Y, MT to chrM, chr1, chr2,...)

I'm currently using JDK 1.7 u79 for compatibility with MuTect 1.7

SortVcf was used as such:

"java -jar picard.jar SortVcf \
INPUT=dbsnp.vcf \
OUTPUT=dbsnp.fixed.vcf \
SEQUENCE_DICTIONARY=hg19.dict

Here's SortVcf's output:

Exception in thread "main" java.lang.NullPointerException
at htsjdk.variant.variantcontext.VariantContextComparator.compare(VariantContextComparator.java:84)
at htsjdk.variant.variantcontext.VariantContextComparator.compare(VariantContextComparator.java:21)
at java.util.TimSort.countRunAndMakeAscending(TimSort.java:324)
at java.util.TimSort.sort(TimSort.java:203)
at java.util.Arrays.sort(Arrays.java:727)
at htsjdk.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:218)
at htsjdk.samtools.util.SortingCollection.add(SortingCollection.java:165)
at picard.vcf.SortVcf.sortInputs(SortVcf.java:154)
at picard.vcf.SortVcf.doWork(SortVcf.java:87)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:187)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)