Filtering options for deep exome target sequencing

Question

[lucakang]

Hi all.

I have been working on deep exome targeted sequencing (1000x). It was captured using illumina library prep. I selected 400 genes from 40 tissue samples to do it. I only used tumor tissue sample, no normal tissue was prepared. I used Mutect 1 and filtered the result with 1. AF >0.1%, 2. DP >30, 3. ExAC <0.01%, SNP 150 filtered. I need to select significant genes from the filter passed genes. However, since there are no normal sample to compare with, germ line mutations were not removed and at this moment there are just too many of them in the list.

Here is my question Is there any method/steps to filter them further?

Thank you.

[Brian Bushnell]

Prior to calling variants, it might be helpful to remove reads that do not align concordantly..