Question: Freebayes variant recalibration and quality filters
1
gravatar for sromero_cordoba
14 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 1.0.2.29-3) 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 • 630 views
ADD COMMENTlink modified 14 months ago by Guy Reeves1.0k • written 14 months ago by sromero_cordoba10
1
gravatar for Guy Reeves
14 months ago by
Guy Reeves1.0k
Germany
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 14 months ago by Guy Reeves1.0k
0
gravatar for Jennifer Hillman Jackson
14 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

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 14 months ago by Jennifer Hillman Jackson25k
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