cd ${youtpath}/PSAP_cluster
Here is an example for trio psap analysis
bash psap/family_psap_pipeline.sh test/test.trio.vcf test/test.trio test/test.trio.ped
Here is an example for singleton psap analysis
bash psap/individual_psap_pipeline.sh test/test.singleton.vcf test/test.singleton test/test.singleton.ped
the scripts under script/ is used for cohort PSAP analysis, it requires tabix vcf.gz and pedigree file for the cohort.
It requires liftover if the vcf file is hg38-based, script for lifting over is here: https://github.com/nzhun/liftover.git