LocusZoom Issuing "No valid markers in VCF file" on a VCF created in Plink 1.9

[sclgood]

Hello, All When I run locuszoom using my own LD file, I have the same problem which was posted as the following https://www.biostars.org/p/194199/

Using user-specified VCF file to calculate LD with reference SNP rs2395623.. Error: no valid markers in VCF file to compute LD from.. Grabbing annotations from SQLite database.. Creating plot.. Warning message: No usable LD information. Deleting temporary files.. Time required: 0d:0h:0m:46s

Actually the reference SNP rs2395623 did exist in vcf file.

The vcf file for LD calculation was created by plink from genotype files. The vcf needs to be phased ?

Thanks Charile Sun

[welchr]

Couple things to check:

• Is there anything in the FILTER column other than PASS? You could try passing --ignore-vcf-filter to see if that helps.

• What do your genotypes look like? Can you give an example of a few of them?