Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
FamSeq vs Polymutt vs DeNovoGear Kath Bioinformatics 3 10-04-2015 02:53 PM
Unable to find ORF for fasta file dena.dinesh Introductions 10 02-19-2015 12:41 AM
denovogear parameter m_elena_bioinfo Bioinformatics 0 07-04-2014 02:09 AM
Unable to find flag in SAM with bowtie2 - but can with BWA yekwah Bioinformatics 3 10-18-2013 08:20 AM
Where is the denovogear output? ihelbig Bioinformatics 0 12-21-2012 12:11 PM

Thread Tools
Old 01-10-2016, 12:08 PM   #1
Junior Member
Location: Czech rep.

Join Date: Jan 2016
Posts: 1
Default Denovogear - unable to find trio

Hello, I am trying denovogear for trio analysis, I started with three .bam files (f1.bam, f2.bam and f3.bam).
First I made bcf file:
samtools mpileup -gDf hg19.fa f1.bam f2.bam f3.bam > output.bcf

then I used my bcf in denovo gear:

./denovogear dnm auto --ped pedfile.ped --bcf output.bcf

PED file:
fam1 f1.bam f2.bam f3.bam 2 1

and I am getting this error:
Unable to find trio. Code 3:3
Exiting !

Any ideas what I'm doing wrong?

Thanks for your advice

stanedav is offline   Reply With Quote

bcf trio, denovogear

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 03:12 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO