Question: Gatk Mutec2 germline resources for mouse
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gravatar for tarekzakaria.badr
16 months ago by
tarekzakaria.badr30 wrote:

Hi everyone,

i am analyzing mouse exome data with mutec2 for somatic variants detection. I am a bit stuck with the germline resources, couldn't find one for mm10. I have used the sagner provided snps and indels for the known sites in Baserecalibator. Is it possible to used them too for the germline AF resourse? and what would be the disadvantage of running Mutec2 without this resource at all? Many thanks in advance

mm10 sequencing gatk • 729 views
ADD COMMENTlink modified 16 months ago by h.mon30k • written 16 months ago by tarekzakaria.badr30

For calling somatic variants without matched normals (that is the keyword you should google to get a background what normal controls are, also see Can you use germline variation calling on a normal embryonic stem cell line? ) please use the search function, this has been asked many times before, starting with Somatic mutation calling without matched normal

ADD REPLYlink written 16 months ago by ATpoint36k

thanks for your reply, i have matched normal for some of my samples, but Mutec2 suggests running the variant calling also with the germline Allele frequency resource which i couldn't find for mm10. Do you know where to find this resource for mm10 or if it would affect the final called variants in a great manner or not?

ADD REPLYlink written 16 months ago by tarekzakaria.badr30

I wanted to ask same question, have you get a solution?

ADD REPLYlink written 16 months ago by ddzhangzz90

unfortunately i couldn't find an AF germline resource suitable for Mutec so far. i have some normal matches though so i tried to filter through them and PON file. another strategy i am considering is calling also through varscan and samtools and gather common variants from all three pipelines but i am not yet sure how good this approach is. Do you also have exome seq from mice tumor samples?

ADD REPLYlink written 16 months ago by tarekzakaria.badr30
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