Reference Genome for mapping and VCF file for Realignment in Yak (Bos grunniens)

Question

[mostafarafiepour]

Hi all,

I have a problem in the SNP Calling stage for Yak (Bos grunniens), that it is related to Reference Genome for mapping and VCF file for Realignment stage. Please help me to find out about Reference Genome and VCF file for Yak (Bos grunniens).

Best Regard Mostafa

[vmicrobio]

Can you be more specific on what you are looking for? variant calling from specific gene, complete genome... What kind of data do you have? You may find a reference sequences on the genebank

[mostafarafiepour]

I could not find the reference genome and VCF file at your link (genebank)??

[vmicrobio]

ok check the links from the answer I just posted for the references. You have to generate your own vcf... What exactly are you looking for? and what kind of data do you have to start?

Answer 1

[mostafarafiepour]

Thanks a lot for your reply, I am trying to run SNP calling for whole genome sequencing data for Yak (Bos grunniens). So, i need to Reference Genome for mapping and VCF file for Realignment stage.

Answer 2

[vmicrobio]

ok from this study you have the data accessible here. Otherwise, whole genome shotgun sequences are available from the genebank : here

[mostafarafiepour]

yes i using this study But the author of the article only said that we used the Bos grunniens as a genome reference, and he did not have a link or an address to download the genome reference.

Answer 3

[mostafarafiepour]

many thanks for your help, But can not I find a specific link to download the reference genome?

[vmicrobio]

you can download fastq files by ftp and do yourself a consensus sequence or use the whole genome shotgun sequences available from genebank