Hi , I am 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 . I checked the eArray Agilent but I didn't find the relevant file. could anybody help me with finding the correct file for this job? thank you.
for those who read this thread because they faced similar problem:
1. The target of SureSelect XT mouse exome is based on UCSC mm9 mouse genome build and a BED file with exon and gene annotation is available on the Agilent eArray website.
2. log into eArray and find the bed file (regions_mm9.bed ) using interval finder.
3. you might need to liftover this file to mm10 => use UCSC leftover tool and correct chains for mm9tomm10 here.