Find variants supported by at least 20 reads freebayes

Question

[kspata]

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!!!

Answer 1

[finswimmer]

Hello,

my understanding of these two options is, that --min-coverage defines how many reads must be on that position before freebayes starts to look whether there are reads that doesn't support the reference. -C defines how many reads must support the non-reference base before checking more criterias.

So what you are looking for is -C. But unless I'm not absolutly sure what an option does, I wouldn't change the default parameters of a variant caller. Does freebayes do any filtering of reads before counting (MapQ, Duplicates,...)? How it does count overlapping paired reads? I don't know. A better way would be to do the variant calling with default parameters and filter your vcf afterwards. It contains the information how many read support the alternate allele.

fin swimmer