Question: The meaning of VAF and LOH in sciclone
gravatar for shiyang93
2.4 years ago by
shiyang9350 wrote:

I want to use the R package SciClone to infer the clonal architecture of my liver cancer data. I have already got the somatic SNV info and allelic specific copy number variation info, but I am not clear about some input info required by SciClone: 1. What does the "regions to exclude" mean? My understanding is: if a region has total_cn = 2, but major_cn = 2 and minor_cn = 0, then I need to write this region in the "regions to exclude" file. Is this understanding correct? 2. In my opinion, the vaf means var_reads/(var_reads + ref_reads). However, when I used ?sciClone in R, it tolds me:

a list of dataframes containing variant allele fraction data for single nucleotide variants in 5-column format: 1. chromosome 2. position 3. reference-supporting read counts 4. variant-supporting read counts 5. variant allele fraction (between 0-100)

Why is the range of vaf between 0-100? (for me, it must be less than 1). What is the definition of this "vaf"?

Could anyone give me some advice? Thanks!


loh vaf wes sciclone • 1.7k views
ADD COMMENTlink modified 2.4 years ago by Chris Miller21k • written 2.4 years ago by shiyang9350
gravatar for Chris Miller
2.4 years ago by
Chris Miller21k
Washington University in St. Louis, MO
Chris Miller21k wrote:

VAF = variant allele frequency, expressed as a percentage between 0 and 100. The most typical use case for Regions to exclude is the case of copy number neutral loss of heterozygosity: that is, an area that has copy number 2 but has the same alleles twice due to uniparental disomy.

ADD COMMENTlink written 2.4 years ago by Chris Miller21k

"the vaf means var_reads/(var_reads + ref_reads)" - Is it right? In example test case vaf always less then var_reads/(var_reads + ref_reads). Why is that? Is this affected by the admixture of normal cells in sample? Does this difference greatly affect clustering? Many thanks! Alex.

ADD REPLYlink written 2.2 years ago by alexander.kononov10

There may sometimes be non-reference, non-primary-variant reads - for example:

1 12345 A T Counts: A: 99 C: 2 G: 0 T: 99 VAF: 49.5%

ADD REPLYlink written 2.2 years ago by Chris Miller21k
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