Missing Variant with 90% AF

[npatel-ah]

Hello,

We are using LoFreq to detect mutation in a SARS-Cov2 sample, which is working quite well. However, we are puzzled with one mutation missed by LoFreq. As you can see in IGV the SNP has a frequency over > 90%. What is strange is that at the exact same position there is a deletion reported with an allele frequency of "0.000294".

I am attaching a bam file here
Sample_POS28048.zip

Thank you.

[npatel-ah]

Actually figured it out. It is due to the strand bias. I used "--no-default-filter" and was able to capture the mutation.

[andreas-wilm]

Glad you figured it out