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Question: SNP names not lining up with VCF data and locations
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gravatar for d.shilling
3 months ago by
d.shilling • 10
d.shilling • 10 wrote:

Analysis of my SNP names obtained from UCSC Main with the locations of my VCF data shows that they are not correct. The called SNPS are +1 base off of the VCF locations. Can anyone tell me where I went wrong and how to correct it. All are using hg38 as the reference database.
bed vcf galaxy • 151 views
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modified 3 months ago by Jennifer Hillman Jackson ♦ 25k • written 3 months ago by d.shilling • 10
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gravatar for Jennifer Hillman Jackson
3 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

VCF datasets have a 1-based start coordinate and BED datasets have a 0-based start coordinate.

FAQs: https://galaxyproject.org/support/ >> Common datatypes explained

Thanks! Jen, Galaxy team
ADD COMMENT • link written 3 months ago by Jennifer Hillman Jackson ♦ 25k
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Thank you Jennifer, Dave

ADD REPLY • link written 3 months ago by d.shilling • 10
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