correct list of capture targets/intervals for SureSelect mouse exome to perform GATK Mutect2

Question

[ati_]

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.

Answer 1

[ati_]

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. done.

Answer 2

[heskett]

hi there. having this exact problem now. what does correct chains mean? i do worry that liftover wont be entirely accurate