This repository contains sequencing scripts that have been used for the paper:
"Exome sequencing identifies rare damaging variants in ATP8B4 and ABCA1 as novel risk factors for Alzheimer’s Disease", Nature Genetics 2022.
The QC procedure used can be found in the supplement of this paper.
- bcftools_split_patches: These patches adapt the splitting operation implemented by BCFTools, and introduce handling for the PGT (phased-GT), PL (phred-likelihood) and AD (read by allele depth) tags.
- dechimerizer: This script will remove soft-clip overhangs of BAM alignments that are (likely) to have been caused by chimeric reads. Includes also a script to generate detailed statistics for BAM files on supplementary reads.
- posterior_prob: Calculation of posterior likelihoods/dosages and adding these to the VCF
- variant_qc_annot: This script annotates the VCF file with a number of QC annotations, for different variant coverage/quality thresholds, and for genotype 0/1 or posterior probabilistic calls.
- burden_test: a stand-alone version of the burden test as used in the publication. Variant prioritization based on VEP/Loftee/transcripts, and with genotype sampling based on posterior probabilistic calls.
