High Confidence truth without NeuDiscovered for SEQC2 validation data tumor-normal calling

The SEQC2 ground truth dataset included one SNP that was discovered by NeuSomatic. This variant was not annotated with a INFO/TVAF field which is needed for the VAF comparison in our workflow. We decided to remove this variant. $ wget https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/seqc/Somatic_Mutation_WG/release/latest/high-confidence_sSNV_in_HC_regions_v1.2.vcf.gz $ zcat high-confidence_sSNV_in_HC_regions_v1.2.vcf.gz | awk -F'\t' 'BEGIN {OFS="\t"} /^#/ {print; next} $8 !~ /(^|;)NeuDiscovered($|;)/ {print}' | bgzip > high-confidence_sSNV_in_HC_regions_v1.2.rmNeuDiscovered.vcf.gz $ bcftools view -H high-confidence_sSNV_in_HC_regions_v1.2.vcf.gz | wc -l39560$ bcftools view -H high-confidence_sSNV_in_HC_regions_v1.2.rmNeuDiscovered.vcf.gz | wc -l39559