vcf to bed bim fam

[Atoosa Samani]

Hi I used this code to convert vcf to bed bim bam files 

plink2 --vcf 302_birds.vcf.gz --make-bed --out 302_birds_binary -allow-extra-chr

This is the error I got. 

Error: 302_birds_binary.bim cannot contain multiallelic variants.

How can I solve this?

Is there any way to ask plink to ignore nonbinary sites?

[Christopher Chang]

Three options:

1. Use --make-pgen/--pfile instead of --make-bed/--bfile.  This is the preferred solution if it's compatible with your workflow.

2. Filter multiallelic variants out with "--max-alleles 2".

3. "Split" the multiallelic variants with e.g. "bcftools norm".  Analysis results for the split variants may be distorted.

[Amod Kumar]

Hi..

I am using Plink v1.9 to see runs of homozygosity. For generation of vcf files, I used BWA MEM for allignment and GATK (Haplotypecaller, CombinedGVCF, GenotypeGVCF and Hard filtration). I converted these files into binary PED and called ROH using --homozyg command.

I got results: --homozyg: Scan complete, found 0 ROH.

Any help would be highly appreciable.