The result VCF file should contain all the differences between hg38 and hg19. Modify the paths to ChainToVCF.jar, hg19ToHg38.chain and hg19ToHg39-SNP.bgr if needed. hg19ToHg39-SNP.bgr > hg19ToHg38_complete.vcf You can also transfer funds to a The Cash app doesnt charge a fee to send, request or receive personal payments from a debit card or a bank account, or for a.
If any details do not match, you can update them on our app or website by visiting the My Details section. hg19ToHg38.chain -source hg19 -target hg38 -bgr. Download the app and create an account with your email address.Put the file generated in the previous chapter into the same directory as ChainToVCF and the chain file.įrom there open a terminal, and run the following command: Select hg19 when prompter to select a second layer and select an empty track for the result.įigure 2: Save layer Adding the SNPs to the VCF File Right click on the track handler of the hg38 track handler and select the hg38 layer at the bottom of the contextual menu and then select the Compare Sequences option (figure 1). Use the VCF generated during the previous phase instead of the one provided for the tutorial.Īt the end of the tutorial you should end up with a sequence layer for hg19 and a sequence layer for hg38. You first need to go through the following tutorial hg19_GRCh38/hg38_Multi-Genome_Tutorial. To add SNPs to the VCF file we need to extract the remaining differences from the sequences of hg19 and hg38. Generate a BGR File Containing the Remaining Differences Between hg19 and hg38 Using GenPlay GenPlay can generate a BGR file containing these differences.Īfter that, we will use use the ChainToVCF program previously downloaded to add SNPs to the VCF file. We will first extract the differences between the hg19 and hg38 sequences. The process of adding SNPs to the VCF file can be divided into two parts. In the next step we will add the SNPs to our VCF file.
The resulting VCF will contain all the insertion and deletion of hg19 using hg38 as a reference genome. Modify the paths to ChainToVCF.jar and hg19ToHg38.chain if needed. hg19ToHg38.chain -source hg19 -target hg38 > hg19ToHg38.vcf Then, from a terminal, run the following command: The source code is available at įirst, make sure that Scala is properly installed on your system. Note: ChainToVCF is an open source program.
In order to generate our VCF file we will need the Scala program ChainToVCF available at Generate a VCF with the Insertions and the Deletions Note that the chain file needs to be uncompressed.
hg19 reference file in 2bit format (from the full dataset section): hg19 to hg38 chain file (this file can be found in the LiftOver section): Ģ. All the file are available from the download page of the UCSC genome browser. 3.1 Generate a BGR File Containing the Remaining Differences Between hg19 and hg38 Using GenPlayįirst, let's download the files needed from the UCSC genome browser.