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BGI-shenzhen / LDBlockShow

LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on VCF files
MIT License
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Error: Multiple instances of '_' in sample ID #2

Closed sandipmkale closed 3 years ago

sandipmkale commented 3 years ago

Hello I am getting following error: but don't know how to specify --double-id

Error: Multiple instances of '' in sample ID. If you do not want '' to be treated as a FID/IID delimiter, use --double-id or --const-fid to choose a different method of converting VCF sample IDs to PLINK IDs, or --id-delim to change the FID/IID delimiter.

Please help

hewm2008 commented 3 years ago

Dear @sandipmkale

A: I think something wrong on your VCF file, the sample name ID may be should remove the '_' , so you can try modify the sample name in the vcf First.

B: if the input file is [bed+fam+bim] or [map+ped], you can try to convert the file form by on the command line first. such as for chr1:10000-20000 (bed+fam+bim)
LDBlockShow-1.36/bin/plink --file inprefix --export vcf --out outfix --allow-extra-chr --chr chr --from-bp 10000 --to-bp 20000 --const-fid 0
or [map+ped] LDBlockShow-1.36/bin/plink --bfile inprefix --export vcf --out outfix --allow-extra-chr --chr chr --from-bp 10000 --to-bp 20000 --const-fid 0

then you will get the region vcf file [outfix.vcf ] ,so you check the sample name ID in the VCF file header ,and modify them .and then use this VCF file to follow the [LDBlockshow]
./LDBlockShow-1.36/bin/LDBlockShow -InVCF -Region chr1:10000-20000 -OutPut outPrefix -OutPng -othrPara