Question: What is dbsnp file and how can I find it?
0
gravatar for dsh.shadi
6 weeks ago by
dsh.shadi0
dsh.shadi0 wrote:

Hi,

I want to call the variants of my samples from the bam file using MuSE and I need the dbSNP VCF file. I used Grch38.84 for the reference genome and I need the corresponding dbSNP file. I have some questions.

  1. Is there any general database for all of these files that I can download this file? because I searched a lot but I could not find it. Maybe I don't know the correct keywords.
  2. Should the dbSNP file correspond to the exact version of the reference fast file? even the version? (84)
  3. What is the 84 in Grch38.84? Why there is Grch38.p5 in some places? Can I also use the dbSNP vcf file for Grch38.p5?

Best, Shadi

snp tutorial • 142 views
ADD COMMENTlink modified 6 weeks ago by Kevin Blighe71k • written 6 weeks ago by dsh.shadi0
2

Download full list of SNPs and their coordinates in hg38

ADD REPLYlink written 6 weeks ago by Pierre Lindenbaum134k

Thank you very much. I see this question. which you post. But the link that it suggested does not have exactly Grch38.84. It has Grch38.p7 and I am not sure if they are the same and if I can use it for my version of the reference. Are these tags (versions) important or not?

ADD REPLYlink written 6 weeks ago by dsh.shadi0
1

human_9606_b151_GRCh38p7 is dbSNP release version 151 with co-ordinates for GRCh38.p7

ADD REPLYlink written 6 weeks ago by dare_devil1.4k
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