Open SirKuikka opened 1 month ago
Hm, that is odd. Are you seeing the same problem when annotating your main input VCF with the same plugin? Can you please post the Frameshift.pm file you are using?
Hi,
No, I didn't encounter the same problem when I annotated the main input VCF.
This is the plugin https://raw.githubusercontent.com/griffithlab/pVACtools/v2.0.0/tools/pvacseq/VEP_plugins/Frameshift.pm
Can you please attach your phased VCF to this issue so I can try and replicate this error on my end?
Hi,
Unfortunately I can't give the whole file. If 29779 would correspond to line 29779 in the VCF file, I could test if the error happens with those few variants. I can perhaps give those.
That's ok. Can you try commenting out line 129 in Frameshift.pm? The value of that variable is no longer used anyway so we should be ok to remove/comment out the code that is causing the error.
Installation Type
Docker
pVACtools Version / Docker Image
4.1.1
Python Version
No response
Operating System
No response
Describe the bug
Annotate VCF with VEP (https://pvactools.readthedocs.io/en/latest/pvacseq/input_file_prep/proximal_vcf.html)
While annotating the variants, these errors occur 9 times. First, there's the " lt (<) " error two times then the "addition (+)" error once. Therefore, this happened at three genomic positions.
Use of uninitialized value in numeric lt (<) at /path/plugin_dir/vep_plugins/Frameshift.pm /line 129, <$fh> line 29779. Use of uninitialized value in addition (+) at /path/plugin_dir/vep_plugins/Frameshift.pm line 129, <$fh> line 29779
How to reproduce this bug
Input files
No response
Log output
Use of uninitialized value in numeric lt (<) at /path/plugin_dir/vep_plugins/Frameshift.pm /line 129, <$fh> line 29779. Use of uninitialized value in addition (+) at /path/plugin_dir/vep_plugins/Frameshift.pm line 129, <$fh> line 29779
Output files
No response