Question

vcf builded with build37.fa

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7.7 years ago

Stane ▴ 90

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 • 1.3k views

ADD COMMENT • link updated 7.7 years ago by Emily 24k • written 7.7 years ago by Stane ▴ 90

score 1 · Accepted Answer · 2017-03-21

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7.7 years ago

Emily 24k

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

ADD COMMENT • link 7.7 years ago by Emily 24k

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

ADD REPLY • link 7.7 years ago by Stane ▴ 90

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

ADD REPLY • link 7.7 years ago by WouterDeCoster 47k