Question: Processing WES mouse data using GATK on Terra Bio
1
gravatar for Arko
18 months ago by
Arko30
US/Boston/Boston University
Arko30 wrote:

I'm working with whole exome sequencing data from mouse (mm9) in the fastq format. I have an interval list for the sequencing data as well and I want to obtain VCF files from each sample, using GATK best practices on Terra Bio but GATK best practices are tailored to only to human data, so all the WDL scripts on Terra are tailored towards that.

Anybody have any suggestions on how I could go about this? Elaborate solutions would be much appreciated, thanks!

firecloud mm9 exome gatk terra • 671 views
ADD COMMENTlink modified 15 months ago by ati_10 • written 18 months ago by Arko30

You are asking for elaborate solutions, but provide very few details. Is this the Terra Bio you are referring to? If so, it seems they have customer support, did you try to reach them?

ADD REPLYlink written 18 months ago by h.mon32k

I plan on doing that soon, thought I'd see if the community would have any suggestions first. Thanks!

ADD REPLYlink written 18 months ago by Arko30

See if this TeraBio tutorial is useful. More broad level help topics here.

ADD REPLYlink modified 18 months ago • written 18 months ago by GenoMax96k

Hi , I am also doing somatic variant calling using GATK Mutect2 in a mouse model of melanoma based on mm10 reference. according to standard workflow to generate a panel of normals I need the list of target intervals for the "mouse exome" data which has been generated using "SureSelect XT" (V4?). I checked the eArray Agilent but I didn't find the relevant file. did you already find it ? could anybody help me with finding the correct file for this job?

ADD REPLYlink written 15 months ago by ati_10
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