Question: dbsnp for rat
0
gravatar for Rna-Seq
4.5 years ago by
Rna-Seq50
Japan
Rna-Seq50 wrote:

Hi,

I need to download dpsnp of rat. I used dbsnp ftp site and found under organisms there are two data sets for rat rat_10116 and rat_10118 Are they different strains??

Moreover, dpsnp vcf files for rat has SAO which is defined as follows:

##INFO=<ID=SAO,Number=1,Type=Integer,Description="Variant Allele Origin: 0 - unspecified, 1 - Germline, 2 - Somatic, 3 - Both">

For snps with SAO=0 . Is there any possibility that they are somatic variants??

Any help is appreciated.

Thank you.

 

snp • 1.6k views
ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by Rna-Seq50

I'm not familiar the content of dbSNP rat data, but the 10016/10018 are NCBI Taxonomy IDs. 10116 refers specifically to Rattus Norvegicus and 10118 is Rattus Sp.  So I'd guess these are not different strains, but may differentiate variant sequences annotated specifically to Norvegicus versus those just labelled as Rat without further specification.

ADD REPLYlink written 4.5 years ago by Ahill1.8k

Thank you very much Ahill.

Does anyone know about SAO flag in dpsnp files

 dpsnp vcf files for rat has SAO which is defined as follows:

##INFO=<ID=SAO,Number=1,Type=Integer,Description="Variant Allele Origin: 0 - unspecified, 1 - Germline, 2 - Somatic, 3 - Both">

For snps with SAO=0 . Is there any possibility that they are somatic variants??

 

ADD REPLYlink written 4.5 years ago by Rna-Seq50
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