Monopogen
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KChen-lab
SNV calling from single cell sequencing
Hi, I am running Germline, after successfully running preProcess. I met a few problems. First, when I ran germline, the output showed that I didn't have Java. So, I installed...
Hi, I am running PreProcess and then Germline in a process in nextflow. But for some reason, the job never finish even though all the output files are written to...
Hi Thanks for the tool. It's really nice. One thing I noted is that samtools in your code use old version and mpileup `-t` and `-v` is deprecated in the...
Hi, first, thank you for interesting tool to use in single cell I have a question about SNV output(chr*.putativeSNVs.csv). When I put input bam file, bam file have 8923 unique...
Hello! While running Monopogen, I noticed that it outputs quite a number of different files. I have read in your tutorial that the final output should be in the .phased.vcf.gz...
Thanks for the nice tools. I have been tinkering with it to be able to use the new versions of `samtools` and `bcftools`. I believe this should be correct -...
When I run prepocess.py with a sorted bam file, the following error occurs after some time: ValueError: fetch called on a bam file without index. How do I fix it?
hey I got the error while running preprocess always. could you help me out? ``` [2023-10-17 19:20:15,607] INFO Monopogen.py Performing data preprocess before variant calling... [2023-10-17 19:20:15,607] INFO germline.py Parameters...
Hi, I am trying to run Germline on the example provided in the repository. After successfully running preProcess, I run the following command: python src/Monopogen.py germline -a apps/ -t 1...
``` (monopogen-env) anannapaneni@esb:~/Monopogen$ python ${path}/src/Monopogen.py Traceback (most recent call last): File "/home/anannapaneni/Monopogen/src/Monopogen.py", line 13, in import pysam File "/share/quonlab/workspaces/anannapaneni/anaconda3/envs/monopogen-env/lib/python3.12/site-packages/pysam/__init__.py", line 4, in from pysam.libchtslib import * ImportError: /home/anannapaneni/Monopogen/apps/libcrypto.so.1.0.0: version `OPENSSL_1.0.0'...
