Question: Plink/Seq Denovo Option
0
gravatar for Caddymob
7.5 years ago by
Caddymob980
United States
Caddymob980 wrote:

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?

vcf plink denovo • 2.4k views
ADD COMMENTlink modified 7.5 years ago • written 7.5 years ago by Caddymob980
2
gravatar for Caddymob
7.5 years ago by
Caddymob980
United States
Caddymob980 wrote:

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!

ADD COMMENTlink modified 5 months ago by RamRS28k • written 7.5 years ago by Caddymob980

thanks for following up - always much appreciated

ADD REPLYlink written 7.5 years ago by Istvan Albert ♦♦ 84k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1655 users visited in the last hour