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Hi. I'm unable to use the IndelRealigner java jar. My previous steps were;
1) Convert Bowtie2 paired-end Illumina Reads .sam to .bam
2) Use bedtools to extract pairs that fall within the Hg19 exome.
3) Convert the new .bam to .sam
4) Sort the new .sam via SortSam.jar
5) Mark duplicates via MarkDuplicates.jar
6) Use AddOrReplaceReadGroups.jar
7 ) Use ReorderSam.jar
8) Use RealignerTargetCreator
Untill this far everything went well. Now I'm trying the following command; java -jar GenomeAnalysisTK.jar -T IndelRealigner -R [.fasta] -l [ReorderedSam.bam] -targetIntervals [aligner.intervals] -o output.bam (Also when applying -known and an .vcf file Im producing the same error):
I hope you can help me, because I can't find anything related on google.