I am running muTect with the following parameter, and i have the following errors
java -Xmx8g -jar ~/unixTools/muTect-1.1.4-bin/muTect-1.1.4.jar --analysis_type MuTect --reference_sequence ucsc.hg19.fasta --cosmic GATKDictionary/CosmicCodingMuts_v68_Modified.vcf --dbsnp GATKDictionary/dbsnp_138.hg19.vcf --input_file:normal bamRealigned/Sample_ST1_CC008T_IndelRealigned.bam --input_file:tumor bamRealigned/Sample_ST2_CC008N_IndelRealigned.bam --out Test.stats.out --coverage_file Test.wig.text
I did not provide --intervals option, so it would search on the whole genome.
I get this error:
Error processing chr1:1647928 java.lang.IllegalArgumentException: Comparison method violates its general contract! at java.util.TimSort.mergeLo(TimSort.java:747) at java.util.TimSort.mergeAt(TimSort.java:483)
I even tried running older version of muTect, and still get the error.
Any suggestions how to solve it.