BSF DART - demo trio

This dataset is a trio variant calling cohort to use as demonstration in the BSF DART software. The trio comprises the exome data from the Ashkenazim GIAB dataset (https://www.nature.com/articles/sdata201625): HG002_NA24385_son (ftp data) HG003_NA24149_father (ftp data) HG004_NA24143_mother (ftp data) We re-aligned the original bam files to the GRCh38 genome, ran variant calling using GATK v4 HaplotypeCaller on each sample, merged the resulting gVCF files into a single cohort, generated VCF files for each sample and annotated them using ENSEMBL VEP v100 (you can find below the exact command line). Moreover, in order to inform users regarding variant calling quality, we ran the GATK v3.8 CallableLoci analysis on each bam file using a list of exome targets as target intervals. Finally, for each sample we produced: a bigBed track ({sample}_callable_loci.bb) with callability information for each exome region a file ({sample}_non_callable_regions.tsv) containing annotations for the regions which are not "CALLABLE" calculated using the bsf_variant_calling_coverage.R script Please note, that the bam files in the archive have been downsampled to 30% of the original coverage for illustrative purposes but the variant calling has been run using full coverage. <strong>VEP command line:</strong> <pre><code class="language-bash">vep \ --allele_number --allow_non_variant \ --assembly GRCh38 \ --cache --dir_cache ${path_to_cache} --offline \ --dir_plugins ${path_to_plugins} \ --dont_skip --everything --failed 1 \ --fasta ${path_to_hg38_fasta}\ --flag_pick_allele_gene --force_overwrite --format vcf \ --gencode_basic --hgvsg --exclude_predicted \ --plugin CADD,${path_to_CADD_resources}/hg38/1.6/whole_genome_SNVs.tsv.gz,${path_to_CADD_resources}/hg38/1.6/gnomad.genomes.r3.0.indel.tsv.gz \ --species homo_sapiens --merged \ --tmpdir ./tmp \ --vcf --compress_output bgzip --fork 16 \ --input_file ./BSA_0000_DART_Demo_Trio_cohort.vcf.gz \ --output_file ./BSA_0000_DART_Demo_Trio_cohort.vep.vcf.gz \ --stats_file ./BSA_0000_DART_Demo_Trio_cohort.vep.html \ --warning_file ./BSA_0000_DART_Demo_Trio_cohort.vep.warning.txt;</code></pre>