LD store2 cannot be matched

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3 months ago

peggy • 0

I used the IEU Open GWAS to generate Z file, BGEN file, and BGI file in order to create an LD matrix for FINEMAP. I am a beginner in the field of bioinformatics. I have tried various ways, but I still failed. I sincerely want to know where the problem is.

this is vcf I use ,I selected the positions around lead SNPs within a 500 kb range. enter image description here

this is Z file. enter image description here

this is begn file. enter image description here

this is the problem I am facing on. enter image description here

FINEMAP LDstore2 • 318 views

ADD COMMENT • link 3 months ago by peggy • 0

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You can use qctool to output snpstat files and you will have the A1/A2 column, use those to link back to your .z file : )

ADD REPLY • link 3 months ago by landscape95 ▴ 190

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The question I want to ask is why bgen file can not be matched with z file. If I use qctools, this question will be resolved?

ADD REPLY • link 3 months ago by peggy • 0

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It seems ldstore2 require strict agreement between z and bgen, I usually do that with qctools and haven't failed so far : )

ADD REPLY • link 3 months ago by landscape95 ▴ 190

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