Hi there,
I'm trying to produce a list of possible indels using the GATK Realigner Target Creator. I have the latest version of hg19.fasta as my reference and db135.vcf file as my known indels file. I have removed all the chr tags so my chromosomes are intergers (1 - 2 - 3...) but for some reason my reference fatsa file after being indexed is sorted 1 2 3 4 5 6 7 X 8 9 10 11 12 13 14 15 16 17 18 20 Y 19 22 21 M. I cant find any way of getting GATK to run with the data in this format and I have no idea how to change the file, using 'sort' doesn't work?
Any help would be much appreciated - Thanks H
I'm trying to produce a list of possible indels using the GATK Realigner Target Creator. I have the latest version of hg19.fasta as my reference and db135.vcf file as my known indels file. I have removed all the chr tags so my chromosomes are intergers (1 - 2 - 3...) but for some reason my reference fatsa file after being indexed is sorted 1 2 3 4 5 6 7 X 8 9 10 11 12 13 14 15 16 17 18 20 Y 19 22 21 M. I cant find any way of getting GATK to run with the data in this format and I have no idea how to change the file, using 'sort' doesn't work?
Any help would be much appreciated - Thanks H
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