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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 http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.NullPointerException