The fast way to remove all the multiallelic SNPs in plink2

[Shicheng Guo]

Hi All, 

Now, plink2 has the ability to save all the multiallelic SNPs. Please share the fast way to remove all the multiallelic SNPs in plink2. 

Thanks. 

Shicheng

[Christopher Chang]

plink2 --pfile ... --max-alleles 2 --make-pgen --out ...

[takiy berrandou]

Dear all,

I think this work only if ALT column contain 2 or more alleles. However, in most VCFs and Pfile (eg, 1000G in ressource ) the multiallelic variants are stored each one in different row with one REF and one ALT. So, in this case what would be the solution with Plink2 only? 

Previously, in case of VCF I used BCFtools with norm module to collapse multiallelic from multi rows to one row then i use plink2 --vcf ... --max-alleles 2 --make-pgen --out ... cause it is realy fast

Best regards

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[Christopher Chang]

plink2 will have a function to join this type of multiallelic variant back together soon.  For now, you'd use "--export bcf", use bcftools norm to do the job, and then --bcf to retrieve the results.

On Sunday, March 15, 2020 at 10:51:05 AM UTC-7, takiy berrandou wrote:

Dear all,

I think this work only if ALT column contain 2 or more alleles. However, in most VCFs and Pfile (eg, 1000G in ressource ) the multiallelic variants are stored each one in different row with one REF and one ALT. So, in this case what would be the solution with Plink2 only? 

Previously, in case of VCF I used BCFtools with norm module to collapse multiallelic from multi rows to one row then i use plink2 --vcf ... --max-alleles 2 --make-pgen --out ... cause it is realy fast

Best regards

Le ven. 13 mars 2020 à 17:19, Christopher Chang a écrit :

plink2 --pfile ... --max-alleles 2 --make-pgen --out ...

On Friday, March 13, 2020 at 9:01:13 AM UTC-7, Shicheng Guo wrote:

Hi All, 

Now, plink2 has the ability to save all the multiallelic SNPs. Please share the fast way to remove all the multiallelic SNPs in plink2. 

Thanks. 

Shicheng

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[takiy berrandou]

Great news, thank you.

Takiy

Le dim. 15 mars 2020 à 18:57, Christopher Chang <chrch...@gmail.com> a écrit :

plink2 will have a function to join this type of multiallelic variant back together soon.  For now, you'd use "--export bcf", use bcftools norm to do the job, and then --bcf to retrieve the results.

On Sunday, March 15, 2020 at 10:51:05 AM UTC-7, takiy berrandou wrote:

Dear all,

I think this work only if ALT column contain 2 or more alleles. However, in most VCFs and Pfile (eg, 1000G in ressource ) the multiallelic variants are stored each one in different row with one REF and one ALT. So, in this case what would be the solution with Plink2 only? 

Previously, in case of VCF I used BCFtools with norm module to collapse multiallelic from multi rows to one row then i use plink2 --vcf ... --max-alleles 2 --make-pgen --out ... cause it is realy fast

Best regards

Le ven. 13 mars 2020 à 17:19, Christopher Chang a écrit :

plink2 --pfile ... --max-alleles 2 --make-pgen --out ...

On Friday, March 13, 2020 at 9:01:13 AM UTC-7, Shicheng Guo wrote:

Hi All, 

Now, plink2 has the ability to save all the multiallelic SNPs. Please share the fast way to remove all the multiallelic SNPs in plink2. 

Thanks. 

Shicheng

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