low coverage & BAF plots have three peaks
our last sequencing run (WES, ILLUMINA) gave us low coverage for our samples (still we do not know why!). When I tried to produce the density for the b-allele frequency (calculated from the vcf files), the plots appeared to have three peaks instead of one. What could be the explanation for this? and could this help explain the low coverage we have?
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Please share the figures.
here is a link to the figure.
all others with three peaks are similar to this one.
Can you provide some further context about what you are doing? For example, you mention that the coverage was "low" - how low is "low"? id you reduce QC filtering thresholds in response to that?
Also, are you following some tutorial or published work