SNP and Indels
Single Nucleotide Polymorphisms (SNPs) and DNA insertions and deletions
(indels), were identified using Genome Analysis Tool Kit 4 (GATK4)
(4.3.0.0). Sequences were aligned with grcm38
(https://www.gencodegenes.org/mouse/release_M14.html) with BWA-2
(0.7.17-r1188). Duplicates were marked by using GATK4
MarkDuplicatesSpark. Samtools (1.16.1) was used for sorting the
mitochondrial genome. Picard, R (4.2.0) and Samtools were used for
Collect Alignment & Insert Size Metrics. GATK4 was used for Variants
calling, Extract SNPs & Indels, Filter SNPs and Indels, and Base
Quality Score Recalibration (BQSR). Further vcf files were aligned and
marked for SNP and Indels using the integrative genome viewer (IGV)
software (2.16.0).