1. All samples were checked with fastqc 0.11.9 with this command:

2. A report was then generated with multiQC 1.9 note: available on io

3. Each sample was passed through Intelliseq Germline Pipeline (ver 1.8.3) up to the variant calling modules see wdl here.

1. WGS analysis (burden test etc.)
2. PRS analysis

*notes:

Fastq sample names have two parts and both form the ID. For example, sample B156 has the following fastqs: DP8400011742BL_L01_579_1.fq.gz DP8400011742BL_L01_579_2.fq.gz While sample B522 has the following fastqs: DP8400011021BR_L01_579_1.fq.clean.fq.gz FP100001057TR_L01_579_1.fq.clean.fq.gz DP8400011021BR_L01_579_2.fq.clean.fq.gz FP100001057TR_L01_579_2.fq.clean.fq.gz (Both have the 579 id!)

The original location of each fastq and thus assignment to samples is avaliable in the md5.txt file in the data/fastq folder on io. This file does not contain the B539 sample as it was sequenced separately and has its own md5.txt file.

1. io:

• two example bams
• fastqs
• fastqc files with multiqc report
• all vcfs
• joint vcf with GTS

2. cyfronet (Prometheus):

• all bams
• gvcfs
• vcfs
• external-data (gene lists used in the analyses and database of allele frequencies from 900 Polish genomes for reference)
• hail-mts (intermediate files in hail format, easily exportable as vcfs)
• joint-vcf