Question: Convert Vcf From Hg18 To Hg19 Using Liftovervcf.Pl
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gravatar for Raony Guimaraes
8.9 years ago by
Raony Guimaraes100 wrote:

Hello I'm trying to convert my vcf file from 1000 genomes pilot study 2 (trios) that I believe was annotated with hg18 to hg19 using this Broad Tool:

http://www.broadinstitute.org/gsa/wiki/index.php/LiftOverVCF.pl

At this directory I found: ftp://ftp.broadinstitute.org/Liftover_Chain_Files/

Index of /LiftoverChainFiles/

b36tob37.chain 366 kB 7/27/11 10:13:00 AM b37tob36.chain 175 kB 7/27/11 10:13:00 AM b37tohg18.chain 649 kB 7/27/11 10:13:00 AM b37tohg19.chain 1.8 kB 7/27/11 10:13:00 AM hg18tob37.chain 371 kB 7/27/11 10:13:00 AM hg19toHg18.chain 652 kB 7/27/11 10:13:00 AM

Now, What is the difference between b36tob37.chain and hg18tob37.chain ?

Which one i should use in this case ?

vcf conversion liftover hg • 3.5k views
ADD COMMENTlink modified 5.9 years ago by Biostar ♦♦ 20 • written 8.9 years ago by Raony Guimaraes100

Isn't the chromosome naming different? Hence the need for different chain files. You should use the naming that matches your file.

ADD REPLYlink written 5.9 years ago by Istvan Albert ♦♦ 84k
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