Plink/Seq Denovo Option

Was looking at the PLINK/SEQ package today for pulling out denovo variants and munging around in my VCFs. The manual really has nothing on the denovo functuib, and testing the command, I get this... Any ideas what all these mean?

pseq MyTest.vcf denovo --param 
pseq error : expect --param DP(kid) DP(par) PL(kid) PL(par) AB(kid,lwr) AB(kid,upr) AB(par,upr)

DP(kid) DP(par) PL(kid) PL(par) AB(kid,lwr) AB(kid,upr) AB(par,upr) -- Huh?

plink vcf denovo

• 4,026 views • link

written 13.5 years ago by Caddymob

1 answer

I figured it out. Here's the steps... Key is to load in your VCF first then annotate the pedigree.

pseq proj1 load-vcf --vcf  MY.vcf
pseq proj1 load-pedigree --file msa.fam 
pseq proj1 denovo > MYdenovo.megaLists.txt

Easy!

• 92 views • link

updated 6.4 years ago by Ram

• written 13.5 years ago by Caddymob

thanks for following up - always much appreciated

• 0 views • link

written 13.5 years ago by Istvan Albert