Plink/Seq Denovo Option

Question

[Caddymob]

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?

Answer 1

[Caddymob]

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!

[Istvan Albert]

thanks for following up - always much appreciated