Test validation datasets

[marc-sturm]

Papers:

• Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing - Nature Biotechnology
• Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing - Nature Biotechnology

Command used in SAREK:

bcftools view -f 'PASS,.' \                    
HCC1395T_${sample}_vs_HCC1395N_${sample}/HCC1395T_${sample}_vs_HCC1395N_${sample}.strelka.vcf.gz \
-o ${results_folder}${mapper}_PASS_HCC1395T_${sample}_vs_HCC1395N_${sample}.strelka.vcf

 rtg vcfeval -c ${results_folder}${mapper}_PASS_HCC1395T_vs_HCC1395N_${sample}.strelka.somatic_${type,,}s.vcf.gz \
                     -b ./reference_files/somatic_ref/high-confidence_s${type}_in_HC_regions_v1.2.vcf.gz \
                     -o ${results_folder}${mapper}_${sample}_strelka_${type,,}/ \
                     -t grch38.sdf \
                     -e ./reference_files/somatic_ref/High-Confidence_Regions_v1.2.bed \
                     --squash-ploidy --all-records --sample=ALT \
                     --bed-regions ./reference_files/S07604624_Padded_Agilent_SureSelectXT_allexons_V6_UTR.bed