kaichop
commented
4 years ago you can directly analyze this file in ANNOVAR. Read quick start-up instructions for commands.
On Thu, Jun 25, 2020 at 6:38 AM amrita1983 notifications@github.com wrote:
Hi, I have a file with this format in bed with 689916 lines
Chr Start End Ref Alt GIV_Indian_AAF
1 12673 12673 G A 0.001295 1 12719 12719 G C 0.001943 1 12783 12783 G A 0.03433 1 13165 13165 A C 0.001295 1 13273 13273 G C 0.01684 1 13281 13281 C G 0.001943 what I want is the annotation of these coordinates, tried a lot of tools not helping me as they are variant positions with the same start and end. I would like to use annovar on this to get the annoation, is there any way to get it done in annovar as it is not in vcf format. Need urgent help.
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Hi, I have a file with this format in bed with 689916 lines
Chr Start End Ref Alt GIV_Indian_AAF
1 12673 12673 G A 0.001295 1 12719 12719 G C 0.001943 1 12783 12783 G A 0.03433 1 13165 13165 A C 0.001295 1 13273 13273 G C 0.01684 1 13281 13281 C G 0.001943 what I want is the annotation of these coordinates, tried a lot of tools not helping me as they are variant positions with the same start and end. I would like to use annovar on this to get the annoation, is there any way to get it done in annovar as it is not in vcf format. Need urgent help.