Question: Freebayes variant recalibration and quality filters
gravatar for sromero_cordoba
17 months ago by
sromero_cordoba10 wrote:

I am working on freeBayes pipeline for variant calling on BRCA sequence aligned with BWA and I have some questions: 1. The pipeline of FreeBayes bayesian genetic variant detector (Galaxy Version includes variant recalibration?? 2. I am not sure about the cutoff of the variant quality filters. I am using the following suggested hard filters (Presentation from Erik Garrison) a. QUAL > 1 b. QUAL / AO > 10 c. SAF > 0 & SAR > 0 d. RPR > 1 & RPL > 1 Someone has a better suggestion about the filters?? I am doing the filters over the vcf file resulted as output, but I am not sure how to set them in the freebayes prompt of galaxy.

I would appreciate any suggestios, Thanks Sandra Romero

variant calling galaxy • 834 views
ADD COMMENTlink modified 17 months ago by Guy Reeves1.0k • written 17 months ago by sromero_cordoba10
gravatar for Guy Reeves
17 months ago by
Guy Reeves1.0k
Guy Reeves1.0k wrote:

H Sandra There is no possibility of base recalibration with freebayes (this is mostly a GATK thing, personally I think the circumstances where it makes a difference are quite limited).
Personally I run with the default parameters with an DP filter appropriate for samples the and MAPQ>20. As with Mpileup path it is often a good idea to call widely all probable variants and then filter the .VCF (e.g. using SNPsift). If you have a golden SNP dataset this can be used here to see what might be appropriate filtering criterion.

CHeers Guy

ADD COMMENTlink written 17 months ago by Guy Reeves1.0k
gravatar for Jennifer Hillman Jackson
17 months ago by
United States
Jennifer Hillman Jackson25k wrote:


On the Freebayes tool form, set the option Choose parameter selection level to be 5. Full list of options.

Each is labeled with a short label and underlying tool's command-line analog (what you will find in the Freebayes' tool manual).

Thanks, Jen, Galaxy team

ADD COMMENTlink written 17 months ago by Jennifer Hillman Jackson25k
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