MAF filter question

[stacyrousse]

Hi ! Thanks for the development of NanoCaller :) I was wondering, how does the filter for MAF work exactly ? Since only one sample is called at a time, how can the software calculate an accurate MAF ? Thank you !

[umahsn]

Hi,

NanoCaller does not report minor allele frequency. MAF Are you referring to --min_allele_freq parameter specified when running NanoCaller? Because that refers to "minimum alternative allele frequency" threshold that is used t select candidate sites for SNP calling. Specifically, it means the minimum percentage of reads at a genomic position that should have a non-ref base in the given sample for it to be considered as candidate site.

Or are you referring to VF tag in FORMAT column? VF is defined in the header as: "Alternative allele frequency in the order listed", which is just the percentage of reads that have the alternative allele at a position in the given sample.

Let me know if you have further questions.

Best,
Umair

[stacyrousse]

Thank you for your response, I am sorry I indeed misunderstood --min_allele_freq tag for MAF filter. Thanks for elaborating :)