Convert Vcf From Hg18 To Hg19 Using Liftovervcf.Pl

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 ?

conversion liftover vcf hg hg

• 4,973 views • link

updated 11.8 years ago by Biostar

• written 14.7 years ago by Raony Guimaraes •

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

• 1 views • link

written 11.8 years ago by Istvan Albert

0 answers

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