Open whiffen-cann opened 2 years ago
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.
Hi @etal,the sequencing method for my cfDNA samples is enriching the whole exome。
I have used the following options : subcommand:
segment --drop-low-coverage --drop-outliers
call -filer ci ,sem ,ampdel,cn