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ultimatesource / denovogear

A program to detect denovo-variants using next-generation sequencing data.
http://www.nature.com/nmeth/journal/v10/n10/full/nmeth.2611.html
GNU General Public License v3.0
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Information used from vcf file by dng dnm? #125

Closed aistrand closed 8 years ago

aistrand commented 8 years ago

Hi,

I would like to know which fields/information dng dnm uses from the input vcf file to determine which sites have putative mutations. I understand the program uses genotype likelihoods (and also read depth for filtering purposes). Genotype likelihoods are present in the FORMAT field for each individual. Are there any other fields that are used by your program/model?

Thanks, Alva

reedacartwright commented 8 years ago

@gatoravi @dconrad, do you know?

gatoravi commented 8 years ago

Hi, The model uses the PL field which contains the likelihoods, it also uses the depth and mapping quality fields for filtering. Avi

kaeldai commented 8 years ago

DNM can also use the I16 mapping qualities, inserted as a list in the INFO field. However it's not required.

aistrand commented 8 years ago

OK great, thanks!

aistrand commented 8 years ago

What are the specific filtering criteria that are used for read depth (rd_cutoff) and mapping quality? Could not find specific values in your documentation.

gatoravi commented 8 years ago

When you run the program with no parameters you will see that the default read-depth cutoff is set to 10, this is the value within the parantheses, 

  -R [ --rd_cutoff ] arg (=10)       Read depth filter, sites where either one
                                     of the sample have read depth less than
                                     this threshold are filtered out

You can set this value to something else(same goes for --pp_cutoff). I think the mapping quality filter has been turned off for now.

reedacartwright commented 8 years ago

Alva, I think your question has been answered, so I will close this thread.

aistrand commented 8 years ago

Sure, thanks!

Alva

On Wed, Apr 6, 2016 at 9:06 PM, Reed A. Cartwright <notifications@github.com

wrote:

Alva, I think your question has been answered, so I will close this thread.

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/denovogear/denovogear/issues/125#issuecomment-206640661