Can Platypus detect variants with low allele fractions?

[Jacquelyn Reuther]

Hi,

We recently sequenced a cell line with a known BRAF V600E mutation with a variant allele fraction of approximately 6%. Shown below is the BAM file used (generated by BWA) as input for platypus variant calling. This variant is clearly represented in the BAM files at a VAF of 7% but the variant was not called by Platypus. Is platypus able to call variants of low allelic fractions? For reference, this data was generated from a sample undergoing hybridization captureand a was aligned by BWA with duplicate reads are marked by Platypus (reads shown in IGV screenshot are indicative of the true deduplicated read count). Thanks for your help!

Jacquelyn