Question: B Allele Frequency (VAF) Segmentation Analysis
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gravatar for stachele
16 months ago by
stachele0
stachele0 wrote:

I am working with BAFsegmentation software (http://baseplugins.thep.lu.se/wiki/se.lu.onk.BAFsegmentation). I started with VCF files from exome sequencing, merged all sites and converted to a bed file. Then, I calculated b allele frequency at every site in this cumulative bed file for every sample and prepared a per-sample input file with corresponding Log R Ratios derived from a prior SCNA analysis.

The above program calculates allelic imbalance by performing segmentation using input B Allele Frequency or rather mBAF (mirrored B allele frequency--BAF reflected across the 0.5 axis) and Log R ratios for sites across the genome.

The output of this BAFsegmentation is very confusing. Could anyone tell me why I might observe mBAF segments at levels between 0.5 and 1 where copy number appears to be zero. Also, why do I observe peaks rather than longer segments. Would that make sense biologically?

Please let me know what additional files I can provide to help. Thanks!

SCNA_segmentation_plot Allelic_imbalance_by_sample

ADD COMMENTlink modified 16 months ago • written 16 months ago by stachele0

If possible, can you show the raw minor allele frequency plot (using scatter plot format of the first figure)?

ADD REPLYlink written 16 months ago by Noushin N530
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