title: Linked-read whole-genome sequencing of NS12911
design: High molecular weight DNA was prepared using the 10X Genomics Chromium Genome Kit following size selection using BluePippin (Sage Science). After sequencing, FASTQ files were generated from raw BCL files using mkfastq mode in the Long Ranger software (version 2.1.3) from 10X Genomics (Pleasanton, CA).  10X Genomics Chromium library index SI-GA-A6 was specified in the required sample sheet file for mkfastq.  Before alignment, the hg38 genome files (not including ALT contigs) were downloaded from ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz and indexed using the mkref mode in Long Ranger. Sequencing alignment and haplotype phasing were performed using the wgs mode in Long Ranger, and the options --sex=male and --vcmode=freebayes were specified.