Hi All,
I wish to find variants covered by at least 20 reads using Freebayes.
The command I was planning to use is as follows:
freebayes -f ref.fasta -F 0.05 --min-coverage 10 -C 20 sample.sorted.bam > output.vcf
According to freebayes help
-C --min-alternate-count N Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position. default: 2
and
--min-coverage N Require at least this coverage to process a site. default: 0
To get variants covered by 20 reads should I change --min-coverage
or -C
? I am doubtful between the two option. What is the difference between --min-coverage
and -C
?
Thanks in advance!!!