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Old 10-09-2013, 01:47 AM   #9
vd4mindia
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Location: Milan

Join Date: May 2013
Posts: 40
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Hi I am facing some problems with the Local realignment step around the indels, I am using the marked bam file after the PCR duplicate marking step but I am getting the following error
##### ERROR MESSAGE: Invalid command line: Cannot process the provided BAM file(s) because they were not indexed. The GATK does offer limited processing of unindexed BAMs in --unsafe mode, but this GATK feature is currently unsupported.

I donot see such errors in the forums. Is it that after marknig the PCR duplicates the bam files needs to be sorted and indexed again? or just indexing and running the target realigner step will be sufficient? Am using the GATK version 2.3 am sure its not a serious problem but am not being able to troubleshoot it. I am trying to get a bit stringent in this local indel realignment so for more specificity am actually using the DBSNP137.vcf , 1000G indel vcf and the Mills and 1000 G gold standard vcf. Please guide me about this. I am using the GATK for the first time and trying to develop a pipeline. Below is the command line am using for this step

java -Xmx14g -jar /data/PGP/gmelloni/GenomeAnalysisTK-2.3-4-g57ea19f/GenomeAnalysisTK.jar -R /scratch/GT/vdas/test_exome/exome/hg19.fa -I SRR062634_marked.sorted.bam -T RealignerTargetCreator -known /scratch/GT/vdas/test_exome/exome/databases/dbsnp_137.hg19.vcf -known /scratch/GT/vdas/test_exome/exome/databases/1000G_phase1.indels.hg19.vcf -known /scratch/GT/vdas/test_exome/exome/databases/Mills_and_1000G_gold_standard.indels.hg19.vcf -o SRR062634_marked.sorted.bam.inervals -S LENIENT
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