Number of Called Variants

[keertikoya]

Hi, we installed Monopogen using git clone:

git clone https://github.com/KChen-lab/Monopogen.git
cd Monopogen
pip install -e .

path="~/Monopogen"
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${path}/apps

We were able to run preProcess successfully on the example 2Mb chr20 file.

Running germline resulted in the error “AssertionError: Program beagle.08Feb22.fa4.jar cannot be found!”

We “wget https://faculty.washington.edu/browning/beagle/beagle.08Feb22.fa4.jar” and “chmod +x beagle.08Feb22.fa4.jar” to get past the error.

Germline then ran successfully with the following command

python ${path}/src/Monopogen.py germline
-a ${path}/apps -t 45 -r region.lst
-p ${path}/example/
-g ${path}/example/chr20_2Mb.hg38.fa -s all -o out

resulting in a phased VCF file for chromosome 20.

However, “bcftools view -H chr20.phased.vcf.gz | wc -l” only results in 1175 lines in the file as opposed to the 23755 number of variants in the tutorial. Should we do anything differently?

Thanks in advance!

[jinzhuangdou]

You have run the example data and only variants from 0-2Mb are included. You can run the whole chromosomes from MAESTER data.