SNP, INDEL and Structural Variant Calling in Mouse Inbred Strains Using Long-Read Sequencing

High-fidelity (HiFi) long-read sequencing using the PacBio platform was performed on 35 classical inbred strains and 4 wild-derived inbred strains. The SNP, INDEL, and structural variant (SV) calling results are provided in the compressed files "SNP.rar", "INDEL.rar", and "SV.rar", respectively. Please decompress the .rar files before use. For SNPs and INDELs, each .vcf.gz file requires further decompression. For SVs, decompression of the .rar file directly yields .vcf files.

Each variant type is provided in two versions: S35, which includes only the 35 classical inbred strains, and S39, which includes all 39 strains (35 classical and 4 wild-derived inbred strains). Structural variants are further categorized into four types: DEL (deletions), INS (insertions), INV (inversions), and DUP (duplications). Detailed information about the strain names and SV calling methods can be found in the accompanying README file.

SNP and INDEL calling were performed using DeepVariant, and the joint callsets were generated using GLnexus.