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vcf builded with build37.fa

Hello, I am new to variant calling, recently I have been ask to analyze some vcf files, most of them are using hg19.fa but some have build37.fa in the header, it seems to be from 2014 and I am not really sure which ref genome it is, is it another name for hg19?

snp
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updated by Emily Emily • written by Stane • Stane

1 answer

The correct name for the genome is GRCh37. hg19 is a nickname.

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written by Emily Emily

Thank you! so I should be able to use GRCh37(hg19) to add the annotations

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written by Stane • Stane

Check that the chromosome identifiers are the same in annotation and vcf, if else you are in for a nasty surprise.

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written by WouterDeCoster WouterDeCoster

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