Plink --Update-Alleles Command Is Not Resulting In Right Way
I am running update allele command in plink but results is not coming in right way: Command is like this: ./plink --file mydata --update-alleles mylist.txt --make-bed --out newfile
but whenever there is a heterozygote in the file its change it into 0 0 not into the given code in the mylist.txt. Is is their any command I am to put with this to identify heterozygote.
• 3,329 views
•
link
updated
by
Biostar
•
written
by
kumar.vinod81
•
written
by
kumar.vinod81
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Assigngin dbsnp RSIDs to Plink .bim files using chr:pos data
written by Hamish •
-
update-chr issues with PLINK 1.9
written by curious
-
Why would you need to specify `--keep-allele-order` and `--a2-allele` when writing a VCF with PLINK?
written by curious
-
PLINK BED format: how interpret 0, 1, 2
written by CaffeSospeso •
-
Merging bed bim fam files from chromosome 1 to 22 at one time
written by khn
-
How to keep the same alleles order between bim file and vcf file?
written by jiumeng66 •
-
How to keep the same allele order of VCF and bim file?
written by jiumeng66 •
-
Forcing A1/A2 alleles in PLINK in a VCF phased file
written by GabrielMontenegro
-
PLINK: Not sure how to go about creating the "mylist.txt" file for the --update-alleles command
written by wondereye •
-
Accounting for problem SNPS when merging multiple plink files
written by lhvkl •
It is a straightforward command and it should work, it could be useful if you could give us a sample
mydata.pedandmylist.txtfile.