Question: Convert matrix in numeric format to genotype format
0
gravatar for shinken123
19 months ago by
shinken12390
México
shinken12390 wrote:

Hi All,

I want to convert a matrix in numeric format, 0 for homozygous reference allele, 1 for heterozygous and 2 for homozygous alternative to a genotype matrix, if it is possible to a vcf file. Do you know any tool to do it?

Best Wishes,

Eric

snp • 937 views
ADD COMMENTlink modified 19 months ago by chrchang5237.1k • written 19 months ago by shinken12390
0
gravatar for chrchang523
19 months ago by
chrchang5237.1k
United States
chrchang5237.1k wrote:

If your matrix is variant-major (i.e. each line has one variant, each column has one sample), it shouldn't take too much work to manipulate it into a form that plink 2.0 --import-dosage (see http://zzz.bwh.harvard.edu/plink/dosage.shtml for a description of the expected format, and http://www.cog-genomics.org/plink/2.0/input#import_dosage for --import-dosage syntax) can read; adding "--export vcf" to the same command line will then give you your VCF.

If it's sample-major, you'll probably need to transpose it first.

ADD COMMENTlink written 19 months ago by chrchang5237.1k
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