I have human DNA samples isolated from tissue and from plasma, which were targeted sequenced on Ion Torrent. I've read some papers and blogs about the data analysis pipeline, but it looks like there is no standard way to do it yet.
The steps to analyse cfDNA (mutation analysis):
- adapters trimming
- quality filtering (Q<20; length<40; remove N bases - are these filters right?)
- mapping to reference with BWA
- add UMI sequences (is this step necessary?)
- Base Recalibration
- calling (with HaplotypeCaller or MuTect2 ?)
- annotated with ANNOVAR
- filter to keep somatic variants (which filters are recommended?)
As I am a noobie to cfDNA analysis, I would really appreciate any help or suggestion.
Thank you very much in advance
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