I am trying to change genomic coordinates for 1kHG data from hg37 to hg38 using CrossMap. I have Crossmap.py in the folder CrossMap at path /fs/projects/..../CrossMap/bin/CrossMap.py. I have never run a python script before. I understood that I am supposed to set python3 path to run this script. I used the following command to set python path in a folder one path above CrossMap using:
export PATH="$PATH:/usr/local/bin/python3" and then run the following command to change the coordinates:
path/CrossMap.py vcf <chain_file> <input.vcf> <refgenome.fa> <output_file> The command seems to run as I do not get any warning or error but I don't get any log or output for this. Any suggestions or ideas are highly appreciated.