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Number of SNPEff variants before filter is more than the actual variants number

Hi everyone,

I used SNPeff to annotate horse SNPs and Indels and found a strange phenomena in the html output. The number of variants (before filter) is larger than the number of lines (which I understand as being the number of SNPs or indels). That is, the number of variants that get analyzed by SNPeff is larger than the number of variants that are actually in the vcf file itself. I don't know where does SNPeff come up with the extra set of variants. I tried to understand this issue by myself but couldn't really wrap my head around it. I would have given an example HTML here but I couldn't see an option to upload one. I would really appreciate any thoughts or ideas as to why this is the case ?.

Thank you

snpeff annotation
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updated by Ram Ram • written by modi2020 • modi2020

Hello modi2020!

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updated by Ram Ram • written by User 59 User 59

1 answer

Are you sure the number of lines you're counting corresponds to the number of variants? Perhaps you can compare the sorted sets of (position, REF, ALT) of the input and output files and ensure that each position is covered without any modification.

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written by Ram Ram

Thank you for your prompt reply RamRS,

Just to clarify the matter a bit more. I am working with INDELs data called on GATK.

Also, the number of lines is 830,370, whereas the number of variants (before filter) is 841,444.

Now, I sorted both the input and output VCF files and counted the number of lines (without the header i.e not counting lines starting with #) both files agreed in that they contain 830,370 lines.Therefore, perhaps what SNPeff defines as a variant isn't necessarily corresponding to a line.

Also, SNPeff output shows that the Number of multi-allelic VCF entries (i.e. more than two alleles) is 10,811. Even when I add this number to the number of lines in the vcf file that doesn't add up to 841,444 variants.

Now, the rest of SNPeff calculations is based on the 841,444 variants.

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updated by Ram Ram • written by modi2020 • modi2020

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