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chr37 VCF files and chr37 reference fasta files seems incompatible for RealignerTargetCreator

daviddeunadaviddeuna Member
edited August 2012 in Ask the GATK team

I had downloaded 1000G_phase1.indels.b37.vcf and Mills_and_1000G_gold_standard.indels.b37.sites.vcf
files and i am using reference genome downloaded form uscs (i need use it because i have access only to BAM files that were generated with this file and novoaling aligner), RealignerTargetCreator detect diferences in naming chromosomes (chr1 vs 1 and different contigs) I rewrite vcf files to adapt the format but i still found problems related with the order in 1000G_phase1.indels.b37.vcf file.
Is there any tools to do this task, if this is not posible wat files i need to use from bundle.

Thanks in advance.

David

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