-
Notifications
You must be signed in to change notification settings - Fork 38
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
VCF file is empty #266
Comments
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Describe the bug
The vcf file is empty, calling in individual (germline) mode
Version
Command
Command line to install octopus:
git clone https://github.com/luntergroup/octopus.git scripts/install.py #all dependencies were in the PATH
Command line to run octopus:
Additional context
just a normal fasta with a bam obtained from mapping with bwa-mem
bwa command:
while read p; do bwa-mem2 mem -R '@RG\tID:foo\tSM:bar' -k 12 -t22 vaga.fa ${p}.R1.fastq.gz ${p}.R2.fastq.gz|samtools sort -m 2G -@24 -o bwa_k10_mapping/${p}.sorted.bam; done <ID
Any idea as why my vcf is empty? The run time is also extremely short, less than 5 minutes, which I find surprising. It makes me the impression it's skipping steps it shouldn't.
I checked a pileup, just in case there would be 0 variant in the alignement (which wouldn't make any sense but who knows, maybe a wrong manipulation), but there are variants.
I can send you the bam file if you wish so.
Thanks a lot
EDIT: removing the -C tag seems to solve the issue. That being said, the time estimate for the analysis is very long. Is there anyway to speed things up?
EDIT; there might be an issue with the uploaded forest file, see here: #259 (comment)
is it the correct file?
EDIT: indeed the forest files can't be downloaded because of data size on github, therefore Octopus in forest mode has nothing to classify anything.
The text was updated successfully, but these errors were encountered: