Working with multi-biallelic rows of VCF in plink

Question

[MAPK]

Hi All, I have a VCF file that I generated after merging INDELS.vcf and SNPs.vcf. I used picard tool to merge these into one VCF as java -jar picard.jar MergeVcfs I=${SNPS} I=${INDELS} O=${BOTH}.

This generates multi-row biallelic VCF (not multiallelic). I was wondering if plink has issues with this file. I preliminary analysis shows that plink gives warnings for variants at the same site, but I am not sure if this is a problem.

Also, can someone please suggest a better way to merge INDELs with SNPs ?

[Ram]

Maybe pipe the output to bcftools -m +any - that should merge multi-allelic records into single records irrespective of if they're SNP records or Indel records.