Processing WES mouse data using GATK on Terra Bio

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4.7 years ago

Arko ▴ 30

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!

Terra GATK mm9 exome Firecloud • 1.6k views

ADD COMMENT • link updated 4.4 years ago by ati_ ▴ 40 • written 4.7 years ago by Arko ▴ 30

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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 REPLY • link 4.7 years ago by h.mon 35k

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

ADD REPLY • link 4.7 years ago by Arko ▴ 30

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

ADD REPLY • link 4.7 years ago by GenoMax 141k

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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 REPLY • link 4.4 years ago by ati_ ▴ 40

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