Entering edit mode
7 months ago
A_heath
▴
160
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!
interesting. have you compared its performance head to head against other similar algorithms? Manta or what have you?