Supplementary data involved in SDrecall manuscript and Github repository

Containing supplementary files used in SDrecall manuscript. 1. The control cohort VCF files containing variants across segmental duplications overlapped with exons. The VCF mapped to hg19 reference genome assembly is the original file and the VCF mapped to hg38 is lifted based on the hg19 VCF file by CrossMap. These VCF files are not directly involved in SDrecall's performance and function. They are only used to identify potential common variants within regions of segmental duplications. Below 4 listed files are directly involved: ngs.SDrecall.control.hg19.norm.vcf.gz ngs.SDrecall.control.hg19.norm.vcf.gz.tbi ngs.SDrecall.control.hg38.norm.vcf.gz ngs.SDrecall.control.hg38.norm.vcf.gz.tbi 2. Test BAM files and their indices used in SDrecall manuscript. The BAM files contain reads from sample HG002, covering known segmental duplications with an average depth of 30. The BAM files are downsampled from the original 300X BAM files that are directly acquired from the Genome In A Bottle project. Below 4 files are directly involved: HG002.SD.deduped.hg19.bam HG002.SD.deduped.hg19.bam.bai HG002.SD.deduped.hg38.bam HG002.SD.deduped.hg38.bam.bai 3. Supplementary data originally stored in SDrecall GitHub public repository. Due to the limitation of data size of public github repository. We compressed the entire subfolder "data" under the github repository to here. The zip file contains 3 types of data in separate sub-folders across 3 human reference genome assemblies: a. "default_target": The default targeting region. By default, SDrecall targets the Challenging Medical Relevant Genes and the BED file containing regions of these genes are directly acquired from the Genome In A Bottle Project. b. "ref_SD": The reference regions of segmental of duplications, directly acquired from UCSC annotation tracks. c. "raw_intrin_align": The intrinsic alignment file containing paralogous sequence variants. The intrinsic alignment is generated by mapping reference genomic sequence against segmental duplications from their homologous counterparts. The mapping is done following the binary format segmental duplication in data type b. Only 1 compressed archive file is directly related: SDrecall_github_data.zip The source code of SDrecall under active maintainence and updates is stored at https://github.com/snakesch/SDrecall