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Plink or vcf 1000 genomes files with INDEL format I/D
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4.8 years ago
1888 • 60
United States

Hi,

I was wondering if there are Plink files (or vcf which can be converted in Plink format) available for 1000Genomes where the alleles are coded as D (deletion) and I (insertion), rather than ACGT, and the names of the INDELs would be chr:pos:I or chr:pos:D instead of chr:pos:alleles.

One way could be to extract INDELs from the vcf 1000 Genomes, change these to I/D for alleles and chr:pos:I or chr:pos:D for names, and then use

--update-name and --update-alleles

in Plink2.

If however there is a vcf file already in this format an easier way could be to make this vcf into Plink format using Plink2. Does anybody know whether this format exists?

Any feedback/suggestions if there is an easier way to do this is very much appreciated.

Thank you

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