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CSB5 / lofreq

LoFreq Star: Sensitive variant calling from sequencing data
http://csb5.github.io/lofreq/
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Missing Variant with 90% AF #112

Closed npatel-ah closed 3 years ago

npatel-ah commented 3 years ago

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".

Sample_igv_POS28048

I am attaching a bam file here Sample_POS28048.zip

Thank you.

npatel-ah commented 3 years ago

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 commented 3 years ago

Glad you figured it out