Attention: Want an end-to-end pipelining solution for GATK Best Practices?

Check out Terra here! For more details on whether this is the right fit for you checkout our blogs here.

Problem with running Mutect2 and CosmicCodingMuts.vcf


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.
To get help, see
Exception in thread "main" java.lang.NullPointerException
at java.util.TimSort.countRunAndMakeAscending(
at java.util.TimSort.sort(
at java.util.Arrays.sort(
at htsjdk.samtools.util.SortingCollection.spillToDisk(
at htsjdk.samtools.util.SortingCollection.add(
at picard.vcf.SortVcf.sortInputs(
at picard.vcf.SortVcf.doWork(
at picard.cmdline.CommandLineProgram.instanceMain(
at picard.cmdline.PicardCommandLine.instanceMain(
at picard.cmdline.PicardCommandLine.main(


Sign In or Register to comment.