Entering edit mode
7.0 years ago
adp7
▴
10
Hi,
I'm trying to analyze a panel of genes in tumor samples using truseq custom amplicon (TSCA) with average depth ~2000X. I was wondering if classic tools like GATK HC, UG, MUTECT are adapted to this kind of data? Is there any extra filtering step to perform because of the PCR amplification? And if is there variant calling settings more suited for deep sequencing approach?
Thanks in advance
Would you consider this to also be the case for exome sequencing?
Depends on the library type. Most exomes are capture-based, so the fragments should be randomly selected. There are some exceptions. For example, Agilent SureSelect is amplicon-based, so it's more like TSCA.
GATK Best Practices has the same section for WGS and WES, since the two are usually so similar.