Question: "count"in the snpEFF html output
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gravatar for lifang5389
5 months ago by
lifang53890
lifang53890 wrote:

Hello,

Does anyone know how the "count" and "percent" was calculated in the snpEFF html output file? It shows my total variant number is "2,670,133", which is exactly the same as I count using other tools. But the count of "MODIFIER " in the "number of effects by impact" part is 5,076,144, much larger than the total number.

Best wishes, fang

snpeff • 199 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by lifang53890

I have only kept the longest transcript in the genes.gff file, removed all sites contained more than one alts before run the snpEFF, but still got the much larger number in the himl file.

ADD REPLYlink written 5 months ago by lifang53890

As far as I know, the number of MODIFIER SNPs reported by SnpEFF does not reflect the number of distinct SNPs classified as MODIFIER. I haven't found in its manual, but I believe SnpEFF count them per gene, which may cause it to count them more than once. For example, if a SNP is downstream of gene A, and within the ORF of gene B, this SNP is MODIFIER in relation to gene A and gene B, and SnpEFF may count it twice. The same could be true for the other numbers of effect impacts given by SnpEFF. Be careful when reporting these numbers.

ADD REPLYlink written 5 months ago by alex.zaccaron0
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