I am struggling with SNP analysis of exome sequencing data of bulk DNA amplified by Repli-g single cell whole genome amplification kit, it looks like our data are full of artefacts. Healthy control (blood DNA) wasnt amplified. Do you guys have some advices about some pattern and types of artefacts it does and the best way how to clean the data? Which filtres do you use in this case?
By now, I found this tool which looks interesting:
and I am going through literature but advices from someone with direct experience would be irreplaceable.
Thak you very much!