Is there any good ideas about which options/method of cnvkit would be recommended when calling CNAs in ctDNA samples? Due to unknown sample purity ,I hava got so much genes and segments in my ctDNA sample with subcommand genemetrics.

[whiffen-cann]

I have used the following options : subcommand：

• segment --drop-low-coverage --drop-outliers

• call -filer ci ,sem ,ampdel,cn

[etal]

It depends on the type of sequencing you're doing for these ctDNA samples. Are you capturing/amplifying a gene panel, enriching the whole exome, or sequencing the whole genome?

You can estimate tumor fraction with PureCN; that might help. Generally, segmetrics --ci --alpha .1 --drop-low-coverage and call --filter ci should help.

[whiffen-cann]

Hi @etal,the sequencing method for my cfDNA samples is enriching the whole exome。