Variants where called following the GATK best practices workflow: Reads were mapped onto GRCh38.86 with BWA mem, and both optical and PCR duplicates were removed with Picard, followed by base recalibration with GATK. The GATK HaplotypeCaller was used to call variants per-sample, including summarized evidence for non-variant sites (GVCF approach). Then, GATK genotyping was done in a joint way over GVCF files of all samples. Genotyped variants were filtered using hard thresholds. For SNVs, the criterion QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0 was used, for Indels the criterion QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0 was used. Finally, SnpEff was used to predict and report variant effects. In addition, quality control was performed with FastQC, Samtools, and Picard and aggregated into an interactive report via MultiQC.

Detailed software versions can be found under Rules.

Calls

Plots

allele-freqs.svg Download

Per variant per sample allele frequency, i.e., m ⁄ n where m is the number of reads supporting the variant allele and n is the total number of reads over the variant allele in that sample.

depths.svg Download

Read depth distribution over variant alleles of each sample.

Quality control