I am using LocusZoom command line tool (version 1.4). I am trying to generate LD from a VCF file I have with whole genome data, as some of the variants I am interested in are not in 1000 genomes, and their LD is therefore not shown.
I am trying to run the following command:
locuszoom --metal METAANALYSIS.nr_1.tbl.locusZoom --build hg38 --markercol "chrMarkerName" --pvalcol "P-value" --refsnp chrV:W --flank 100kb --pop EUR --source 1000G_Nov2014 --prefix 100kb_test --delim " " --svg --ld-vcf chrV_Ckb_Dkb.vcf.gz
My variant "chrV:W" is present in the VCF file coded like this (and the VCF file has been tabixed). :
chrV W chrV_W_A1_A2_b38 A1 A2 33751.6 PASS
(The VCF file only has variants in a region of 1 Mb around the variant of interest.)
The metal file looks like this (not the actual P-value):
chrMarkerName P-value chrV:W 0.8125
Where I have recoded "V" as the chr, "W" as the position, "C" as the start position of the interval, and "D" as the end position of the interval. And the two alleles as A1 and A2.
I get the following error:
Using user-specified VCF file to calculate LD with reference SNP chrV:W.. Error: while calculating LD from VCF file: index SNP position W does not exist in file..
I am using LocusZoom command line tool (version 1.4). I am trying to generate LD from a VCF file I have with whole genome data, as some of the variants I am interested in are not in 1000 genomes, and their LD is therefore not shown.
I am trying to run the following command:
locuszoom --metal METAANALYSIS.nr_1.tbl.locusZoom --build hg38 --markercol "chrMarkerName" --pvalcol "P-value" --refsnp chrV:W --flank 100kb --pop EUR --source 1000G_Nov2014 --prefix 100kb_test --delim " " --svg --ld-vcf chrV_Ckb_Dkb.vcf.gzMy variant "chrV:W" is present in the VCF file coded like this (and the VCF file has been tabixed). :
chrV W chrV_W_A1_A2_b38 A1 A2 33751.6 PASS(The VCF file only has variants in a region of 1 Mb around the variant of interest.)The metal file looks like this (not the actual P-value):
chrMarkerName P-value chrV:W 0.8125Where I have recoded "V" as the chr, "W" as the position, "C" as the start position of the interval, and "D" as the end position of the interval. And the two alleles as A1 and A2.
I get the following error:
Using user-specified VCF file to calculate LD with reference SNP chrV:W.. Error: while calculating LD from VCF file: index SNP position W does not exist in file..Can anyone help me?