This is a test version of Biostars. For the public version, visit https://www.biostars.org.
SNPeff: can I just use hg19?

If I haved used hg38 to call variants and then use SNPeff in combination hg19 to annotate that file, what will happen?

I would expect the output to be totally wrong. Because my positions in the VCF refer to hg38. It could well be that my SNP, which is at position 5000 in hg38 is at position 4000 in hg19 right? So SNPeff would check position 5000 in hg19 instead of position 4000. Am I right with my thinking?

Then why does the SNPeff documentation recommend to use the latest version of hg19? How can you make such a general statement? I think the reference HAS TO BE the same that was used to call the variants or am I wrong here? Because using another reference would result in column 2 of the VCF indicating wrong genomic positions, right??

snpeff reference
• 1,026 views • link
updated by h.mon h.mon • written by Marvin Marvin

Then why does the SNPeff documentation recommend to use the latest version of hg19?

Where does snpEff say this exactly? A link to the relevant documentation would help.

• 1 views • link
written by Ram Ram

1 answer

Yes, you would get wrong annotations, if you get anything at all. You should use the same genome version as you used for the previous analysis steps.

But I don't see snpEff documentation recommending hg19 usage, in fact, I see the exact opposite:

WARNING: Usage of hg19 genome is deprecated and discouraged, you should use GRChXX.YY instead (e.g. the latest version at the time of writing is GRCh37.70)

What I think they are recommending is to use the latest version of the available human genome for all analyses performed, from mapping to variant calling to annotation. However, usually manuals lag behind, and the "latest" version cited in the manual is not the current latest version.

• 1 views • link
written by h.mon h.mon

Log in to answer this question.

More posts like this