Open sclgood opened 5 years ago
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?
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