Best Freebayes parameter for haploid variant detection
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!
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interesting. have you compared its performance head to head against other similar algorithms? Manta or what have you?