Closed Lin-Yuying closed 2 years ago
Can you check to see if this issues persists with the develop
branch?
Hi Reed,
Thanks for your reply. I actually used the Mac version of DenovoGear, and cannot find any branch in the directory. Could you please provide more details of this kind of error? Thanks!
Lin
The source code for the develop branch can be downloaded from here: https://github.com/ultimatesource/denovogear/archive/refs/heads/develop.zip
I suspect that if you aren't getting any out that your read group information in your bam files do not match the information in your pedigree file.
Hi there,
I solved this issue by replacing '=' with samples names in family ped files.
Hi there,
I encountered an issue recently when using dng-call function in DenovoGear v1.1.1 with command line
dng-call -f /home/ref/ref.fa -q 30 -Q 30 --ped FR24.ped P271.mark_duplicates.bam P433.mark_duplicates.bam P444.mark_duplicates.bam ...P452.mark_duplicates.bam -o test.vcf
and also trieddng-call -f /home/ref/ref.fa -q 30 -Q 30 --ped family.ped -s family.samfiles -o test.vcf
. However, there are no output in vcf files in all my analysis, except the header.My family ped files looks like this:
The header in vcf files look like this
Could you help with this? Thanks in advance.