Thank you so much for your valuable answer and time.
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Assembly used in Variant Effect Predictor
Is it alright to use rs ids obtained out of a certain experiment which used ensembl's GRCh37 assembly in a VEP version GRCh38.p12 assembly to obtain its location? Is it relevant to do so?
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I am not able to understand your question properly. But if it is related to the different version of reference genome to be used at different steps of analysis, then I would suggest to use the same version of reference genome in SNP calling as well as effect predictor. Because result differ when version changes.
I have a list of rs ids obtained from a study that used GRCh37 assembly as reference genome. Now, how can I obtain the location of this list of rs ids in GRCh38.p12 assembly? Is it alright to use the VEP GRCh38.p12 version to do so? Does anybody concur?
no. Uday Rangaswamy. Use grch37 VEP: http://grch37.ensembl.org/Homo_sapiens/Tools/VEP
Hi Uday Rangaswarmy,
I agree with the above posts, but would like to add that we also have the 'Assembly Convertor' tool to map coordinates from one assembly version to another: http://www.ensembl.org/Homo_sapiens/Tools/AssemblyConverter?db=core
Best wishes
Ben
How can I map the position of SNP's obtained using Build 37, Assembly Hg19 to GRCh38 assembly. I'm very particular in doing so. Please help.
Is the position of an SNP obtained using Build 37, Hg19 same as that in GRCh38 assembly?
The location of a SNP in GRCh38 and GRCh37 can be different, e.g. rs4988235 in GRCh38: https://asia.ensembl.org/Homo_sapiens/Variation/Explore?r=2:135850576-135851576;v=rs4988235;vdb=variation;vf=194846935 and in GRCh37: http://grch37.ensembl.org/Homo_sapiens/Variation/Explore?r=2:136608146-136609146;v=rs4988235;vdb=variation;vf=3227163
Alright. Thanks for your insight. Or as an alternative, what if I used the rs ids in VEP GRCh38 version? Wouldn't that give me the same location I'd get if I used the assembly converter tool?
You can use our Assembly Converter tool for mapping, as my colleague Ben has mentioned: https://asia.ensembl.org/Homo_sapiens/Tools/AssemblyConverter?db=core The tool allows you to map the coordinates from one genome assembly to another, e.g. you can use the positions of your SNPs in GRCh37 and map them to GRCh38