-
Hello NeoPredPipe developers:
I am using the latest version of NeoPredPipe. I cloned the repo two days ago.
I am using Python 2.7.15 and I am on a Linux box
(Linux version 3.10.0-862.14.4.el…
-
Dear All,
I am running vcf-expression annotator via this command
vcf-expression-annotator $VCF simple_gene_counts.txt custom gene --id-column Geneid --expression-column gerald_C1TD1ACXX_8_ACAGTG.sor…
-
Hi developers, first of all thank you for putting together this resource.
I am trying to run the NeoRecoPo.py and I am getting some errors. Before detailing those errors, I just want to make sure t…
-
* pvactools version: **docker://griffithlab/pvactools:1.5.9**
* Python version:
* Operating System:
**Describe the bug**
This is similar or identical to #571, where we hit [this exception](htt…
-
Hello,
I'm running into an error with OptiType. I'm pasting the lines from the R.optitype.log file below:
0:00:01.97 Generating binary hit matrix.
Traceback (most recent call last):
File "/u…
-
"""
**2. Single somatic MAF file**
• Includes all somatic mutations (point/indels) along with annotation, filtering, FACETS CCFs, neoantigen predictions (neo_* columns from somatic_variants/neoantig…
-
Hi Sebastian,
Was wondering if before the new major release is out, is it easy enough/straightforward to "just" add the transcript IDs in the output of arriba? This is an essential piece of informa…
-
The latest VEP release is 96 (http://grch37.ensembl.org/info/docs/tools/vep/script/vep_download.html#new). However, the `neoantigen.py` script in https://github.com/taylor-lab/neoantigen-dev does curr…
-
We have planned to include an analysis of tumor mutation burden as well as a comparison to the tumor mutation burden of adult tumors in TCGA. This issue is for fleshing out the analysis. The manuscrip…
-
According to the following statement:
> pVACseq makes predictions for all transcripts of a variant that were annotated as missense_variant, inframe_insertion, inframe_deletion, inframe protein_alte…