Working with multi-biallelic rows of VCF in plink
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 ?
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