Best Freebayes parameter for haploid variant detection

Question

[A_heath]

Hi all,

I am using Freebayes for haploid variant detection, and I am wondering what would be the "best" parameters for reliable mutation search.

Here is what I've tested so far:

freebayes -f assembly.fasta -p 1 -F 0.3 -m 30 -q 20 -C 1 --min-coverage 5 -b mapped_reads_sorted.bam -v output.vcf

Should I increase the frequency to

-F 0.5

Or even more? What others parameters can be adjusted?

If you've had any experience with this tool, what worked best for you?

Many thanks for your help!

[LauferVA]

interesting. have you compared its performance head to head against other similar algorithms? Manta or what have you?