- align-vcf.sh
This script takes unaligned bam files from PacBio revio reads and aligns them to a designated reference; uses samtools to index, flagstat (coverage), and analyze sequencing depth of the aligned bams; it also uses pbindex for downstream pacbio analyses; it then performs Sawfish (PacBio) discover and subsequent Sawfish joint-calling for structural variants (SVs) for each individual; zips the files (bgzip) if they are unzipped and indexes (tabix); and then calls small nucleotide variants (SNVs) using Clair3 with the hifi revio setting; finally, the script will perform trio joint-calling for haplotype resolved SVs across a joint VCF.