Hi

I am currently attempting to install MutScape using Conda, but I am encountering difficulties as the installation process seems to be unsuccessful.

I have followed the specified steps, but it appears that there might be an issue with the installation. I would greatly appreciate any guidance or assistance you could provide to troubleshoot and resolve this matter.

Best

Victor

A commonly used NGS pipeline for variant calling is nf-core/sarek The variant callers implemented in this pipeline are Mutect2, Strekla and Freebayes. It would be nice to add support for freebayes into this package to allow for a seemless transition of variant calling into interpretation using MutScape.

Hello, I would like to use your toolkit to analyze ccle maf files. However, the column names are not exactly in the same format as seen in the TCGA.maf. IS there a way to bypass and use it For .eg. CCLe maf file does not have protein position.

Thank you for this tool.

Best,
Shwetha

Hi, I use mutect2 to make vcf file, and put it into MutScape, then I get the error message as the title says.
the step of "Start VCF combination", "Reading TSV file" and "Formalizing VCF files" are passed, and Killed in the step of Start VCF combination (only print Killed), so I do not know what happen.
Thanks for your answer.

Hi,
Thank you for developing this useful tool.
I encountered an error when I tried to install MutScape using quick installation.
The error message is as follows:

===============
Install PyVCF...

Collecting PyVCF
Using cached PyVCF-0.6.8.tar.gz (34 kB)
ERROR: Command errored out with exit status 1:
command: /home/lordaaa/miniconda3/envs/MutScape/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-yhsoj5_v/pyvcf/setup.py'"'"'; file='"'"'/tmp/pip-install-yhsoj5_v/pyvcf/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-g_fi1ew8
cwd: /tmp/pip-install-yhsoj5_v/pyvcf/
Complete output (1 lines):
error in PyVCF setup command: use_2to3 is invalid.
----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

The environment I use is a clean, newly created Google Cloud VM, and the OS is Ubuntu 18.04.6 LTS.
Any suggestions?

Thank you,
Yi-Chen

Hi, the readme indicates a requirement for GRCh37. Does MutScape support vcf files generated with alignment to GRCh38? I presume I would need to track down all the equivalent GRCh38 files and substitute them in the set up.