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Problem with running Mutect2 and CosmicCodingMuts.vcf

Hi

I have project on tumor and normal samples I have trouble in running mutect2. I found I should do sorting step by Picard SortVcf but I got another error.

Please take a brief look at my pipeline and let me know what is the problem :

1- Downloading CosmicCoding and CosmicNonCoding

2- java -jar picard.jar SortVcf I= hg19/CosmicCodingMuts.vcf.gz O=hg19/CosmicCodingMuts_new.vcf.gz SEQUENCE_DICTIONARY=hg19/ucsc.hg19.dict

and I got these errors

Please let me know how can I fix it?

d position: 2:136,873,423
[Fri Jun 23 17:40:13 IRDT 2017] picard.vcf.SortVcf done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=1341652992
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.NullPointerException
at htsjdk.variant.variantcontext.VariantContextComparator.compare(VariantContextComparator.java:87)
at htsjdk.variant.variantcontext.VariantContextComparator.compare(VariantContextComparator.java:22)
at java.util.TimSort.countRunAndMakeAscending(TimSort.java:355)
at java.util.TimSort.sort(TimSort.java:234)
at java.util.Arrays.sort(Arrays.java:1512)
at htsjdk.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:219)
at htsjdk.samtools.util.SortingCollection.add(SortingCollection.java:166)
at picard.vcf.SortVcf.sortInputs(SortVcf.java:168)
at picard.vcf.SortVcf.doWork(SortVcf.java:101)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:205)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:94)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:104)

Answers

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