Detecting Cancer Somatic Mutations From Multi-Sample Low-Pass Wgs Data

Hi All,

Q1. I'm trying to find recurrent mutations (SNPs and indels) from multi-sample (~100) low-pass (3~4x) whole genome sequencing data for a certain cancer type. They are all paired with matched normal samples. What's the best strategy to call somatic mutations from this type of data?

Q2. When calling somatic mutations, do you normally filter out calls from repeat regions?

Thanks in advance.