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AstraZeneca-NGS / VarDict

VarDict
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Reported Allele Frequency AF > 1 #113

Open annaquaglieri16 opened 5 years ago

annaquaglieri16 commented 5 years ago

Hi there, Maybe I am not clear about what the field AF represents but, in the header, it is defined as:

##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">

However, I get values > 1.

Screen Shot 2019-06-04 at 4 15 56 pm

How is that possible?

Thanks,

Anna

PolinaBevad commented 5 years ago

@annaquaglieri16, hello!

It seems that this is an old problem for a very rare case when VD>DP (https://github.com/AstraZeneca-NGS/VarDictJava/issues/92). As a result, AF becomes > 1. Could you please share a small part of BAM file where it occurs? It will be very helpful if it is possible because your case is very good for debugging due to the small number of reads covers this variant.

Thank you a lot!

annaquaglieri16 commented 5 years ago

Thanks @PolinaBevad ,

Unfortunately I cannot right now, since they are patient with restricted access. I am going to check with my supervisor.

Cheers, Anna