What does allele information mean?

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Cynthia Moncada

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Mar 12, 2021, 10:35:49 AM3/12/21

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Hello,

I am loading and aligning my VCF files to the human reference genome and I want to determine whether SNPs/exonic mutations (that have not been previously filtered out) are present in one or both copies of a gene. How can I determine this?

Along with this, can you help clarify what these bolded features mean on IGV?

When hovering over the SNP, I get the following information:

- the alternative allele

- allele count

- total number of alleles

- allele depth (the number of reads that support each of the reported alleles)

Thank you so much.

Helga Thorvaldsdottir

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Mar 12, 2021, 11:59:30 AM3/12/21

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Hi,

The IGV tooltip just shows whatever is in the VCF file.

For more information about what's in the VCF file, see the spec at https://samtools.github.io/hts-specs/VCFv4.3.pdf