locuszoom on a HPC - LD could not be computed for SNP
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2.8 years ago
tacrolimus ▴ 140

Dear Biostars,

I am running locuszoom via the command line on a HPC to investigate GWAS hits. I have created a "metal" file from my association results outputted from a GWAS performed in PLINK1.9.

When running a single region I get the error:

"PLINK did not complete successfully. Please check the log file to see the directory with the log file. Warning: LD could not be computed for SNP chr1:234590242. This SNP does not exist in the genotype files for computing LD from 1000G_Nov2014/hg38/EUR.. Warning: recombination rate table 'reocomb_rate' not found in database, skipping recomb rate lookups in region. No usable LD information"

My script is this: locuszoom --metal [input dile] --build hg38 --pvalcol P-Value --no-cleanup --markercol MarkerName --pop EUR --source 1000G_Nov2014 --build hg38 -chr 1 --start 234588000 --end 234590742 --prefix x

The actual input files I can't show as I work in an airlock environment but they are similar to the example from the locus zoom website and are tab separated. Example below:

MarkerName P-value chr4:401141 9.4e-390

The log files from plink give: Error: No valid variants specified by --ld-snp/ --ld-snps/ --ld-snp-list .

I get a plot but it is very sparse compared to what I am expecting.

Has anyone else encountered this problem before?

Many thanks

locuszoom HPC bash GWAS • 893 views

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