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I'm trying to use the RealignerTargetCreator as a test with 1 know file; 1000G_phase1.indels.b37.vcf. At first the contigs didn't match with my .BAM file (chr1/chr2 vs 1/2), so I adjusted that. Now when running it for the first time; java - jar [path to genomeAnalysisTK.jar] -T RealignerTargetCreator -R [.fasta] -I [.bam] -o [.intervals] -known [path to 1000g_phase1_adjusted.indels.b37.vcf] it gives the following error: "I/O error loading or writing tribble index file for [path to 1000g]". When running it the second time, I get the following error; "Problem detecting index type", because the .idx file is not correctly created.
What am I doing wrong?