Question: SNP names not lining up with VCF data and locations
0
gravatar for d.shilling
4 weeks ago by
d.shilling10
d.shilling10 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 • 64 views
ADD COMMENTlink modified 4 weeks ago by Jennifer Hillman Jackson25k • written 4 weeks ago by d.shilling10
0
gravatar for Jennifer Hillman Jackson
4 weeks ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink written 4 weeks ago by Jennifer Hillman Jackson25k
1

Thank you Jennifer, Dave

ADD REPLYlink written 29 days ago by d.shilling10
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