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Old 12-26-2015, 06:21 AM   #1
Location: barcelona

Join Date: Mar 2013
Posts: 18
Question heterozygosity and allele balance in NGS doubt


I have data from a target enrichment on a few human genes, of course sequenced through NGS. Enrichment, sequencing and data analysis were performed by a private genomic service.

In the VCF file some variants show an allele frequency around 1-2%, but their locus is called as heterozygous. Isn't the variant presence too low to call it as heterozygous?

I am not too acquainted with these kind of analysis, so I am a little confused by this. Could someone please help me out?

Thanks a lot in advance.

marco12345 is offline   Reply With Quote
Old 12-30-2015, 03:51 AM   #2
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Location: Germany

Join Date: Oct 2008
Posts: 412

Why not do some filtering on the data ? Think vcfutils will do this for you.

Generally people might take variants with an allele frequency cutoff of around 22% to be genuine heterozygotes. Sometimes you get a nice 50/50 ratio, but you miss out on a lot of data if you stick to very strict thresholds.

Certainly reporting 1-2% AF as heterozygotes is not great analysis.
colindaven is offline   Reply With Quote

allele, allele frequency, heterozygous, ngs, vcf

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