Francisco De La Vega

I have received a VCF from LowFeq form a collaborator that used it for calling SNVs from a cfDNA targeted sequencing assay at a high depth of coverage. They develop scripts to use UMIs in the adapters to error correct the aligned reads and then produce a BAM file to feed to LowFreq. The aim is to detect somatic variants in the range of 0.5-2% VAF. However, it appears LowFreq not adding the PASS filter tag to variants under ~2% VAF. Further, since these variants are not passed, the genotypes are reported...