plink: vcf to ped

[Xinhui Wang]

I used plink.9 to convert vcf document to ped document with following scripts

./plik  --make-ped  --vcf -***.vcf  --out test

./pliink --bfile test -recode

It is really work for a single vaf file. However, I would liek to work on a list a vcf documents (about 200 samples and each vcf is from one sample).

Do we have a command to run on all  these samples together and get a ped file includeing all samples?

 

[Xinhui Wang]

one thing to add: I only want to foces in a region of sequenece.

[freeseek]

I think you should consider bcftools to first merge the VCF files together. Plink is not meant to work with VCF files. However, merging VCF files has some significant drawbacks that need to be understood first, as regular VCF files do not encode information to differentiate between missing genotype calls and homozygous reference genotype calls.

[huana R]

hi, you could try TASSEL. They have a function to transfer VCF to plink data format.

[freeseek]

Plink works fine importing VCFs (and it is very fast!) and if you need to retain the information at multi-allelic sites you can follow the instructions on this post: http://bit.ly/1sgOcuP