I have run freebayes SNP caller on a whole genome sample.
It is believed to possibly have cells with genomes that have somatic amplifications or deletions. I am interested in identifying "amplified" chromosomes.
The Freebayes output VCF has the "AF" field : "Estimated allele frequency in the range (0,1]"
Here's a plot of the AF field and counts ...
Y axis is count, X axis is AF for SNPs for several chromosomes.
Why is the distribution bimodal? At 0.5 and at 0.47
Note the minor kinks at 0.33 and 0.67, too.
I'm at a loss. Any thoughts?
It is believed to possibly have cells with genomes that have somatic amplifications or deletions. I am interested in identifying "amplified" chromosomes.
The Freebayes output VCF has the "AF" field : "Estimated allele frequency in the range (0,1]"
Here's a plot of the AF field and counts ...
Y axis is count, X axis is AF for SNPs for several chromosomes.
Why is the distribution bimodal? At 0.5 and at 0.47
Note the minor kinks at 0.33 and 0.67, too.
I'm at a loss. Any thoughts?
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