Error in line 96

[itslittman]

I'm not an expert but I think Monopogen.py has an error that results in the incorrect concatenation of the --imputation_panel argument with the filename. Line 96:

imputation_vcf = args.imputation_panel + "CCDG_14151_B01_GRM_WGS_2020-08-05_"

should be:

imputation_vcf = args.imputation_panel + "/CCDG_14151_B01_GRM_WGS_2020-08-05_"

right?

Adding the / made it run without error

[ZiyiWang7]

Hi @itslittman

Thank you for your interest in our package! The code is correct when you input the directory of the imputation reference with the "/" sign, but your way would also work.

Below is the sample code provided in the README section:
python ${path}/src/Monopogen.py germline \ -a ${path}/apps -t 1 -r region.lst \ -p ../example/ \ -g ../example/chr20_2Mb.hg38.fa -s all -o out

In this code, the imputation panel is specified using the -p flag.