Question: Do I need to use hg19 or hg38 reference for performing variant calling analysis and RNAseq analysis?
0
gravatar for bioinforesearchquestions
20 months ago by
United States
bioinforesearchquestions120 wrote:

Dear All,

I need some help on selecting the reference fasta for human genome. Do I need to use hg19 or hg38 reference for performing variant calling analysis and RNAseq analysis?

snp reference dnaseq rnaseq • 1.2k views
ADD COMMENTlink modified 20 months ago by Ashley0 • written 20 months ago by bioinforesearchquestions120
4
gravatar for Vivek
20 months ago by
Vivek1.9k
Denmark
Vivek1.9k wrote:

There is no wrong option here. I believe most of the annotation information has been made available for hg38, so you should be good to go with the newer version.

ADD COMMENTlink written 20 months ago by Vivek1.9k

Thanks Vivek.

1) I am using GATK for variant calling analysis. Where can I download the hg38 version of reference for gate_bundle? 2) For RNASeq analysis, I downloaded the hg38 version of reference from genome's Illumina website.

Do you suggest me any other standard website for downloading hg38?

ADD REPLYlink written 20 months ago by bioinforesearchquestions120

As of now the GATK bundle does not have a hg38 version. So if you want to avoid that hassle, best to go with hg19.

ADD REPLYlink written 20 months ago by Vivek1.9k

Thanks Vivek for help. Then I will go with hg19 version itself.

ADD REPLYlink written 20 months ago by bioinforesearchquestions120
1
gravatar for mastal511
20 months ago by
mastal5111.7k
mastal5111.7k wrote:

You will save yourself a lot of hassle by downloading the genome from GATK, otherwise you will keep getting errors because the chromosomes are not ordered in 'karyotypic' order the way GATK uses them.

https://www.broadinstitute.org/gatk/guide/article.php?id=1215

ADD COMMENTlink modified 20 months ago • written 20 months ago by mastal5111.7k

Dear Mastal,

I have GATK;s hg19 bundle resources. Does GATK bundle provides hg38 resources or not?

ADD REPLYlink written 20 months ago by bioinforesearchquestions120
0
gravatar for mastal511
20 months ago by
mastal5111.7k
mastal5111.7k wrote:

the link that I gave above leads to directories hg38/hg38bundle, so, yes.

ADD COMMENTlink written 20 months ago by mastal5111.7k
0
gravatar for H.Hasani
20 months ago by
H.Hasani580
Freiburg, Germany
H.Hasani580 wrote:

Hi,

as Vivek already said, both options are valid, the question is how does the downstream analysis look like, you might face tools, that can not tolerate one of those...just keep that in mind!

ADD COMMENTlink written 20 months ago by H.Hasani580

I am going to do variant calling analysis using GATK and annovar. I might compare my snps with dbsnp, 1000genomeproject, hap map etc..

ADD REPLYlink written 20 months ago by bioinforesearchquestions120
0
gravatar for Ashley
20 months ago by
Ashley0
China
Ashley0 wrote:

Hi, if the software which the next step's need is hg19, I perfer you to hg19.

ADD COMMENTlink written 20 months ago by Ashley0
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