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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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.vcf file has a GT half-call. #17

Closed PengJia6 closed 2 weeks ago

PengJia6 commented 2 years ago

Hi,

I used LDBlockShow to analysis my vcf file. But I got the following error.

Error: Line 5230 of .vcf file has a GT half-call.
Use --vcf-half-call to specify how these should be processed

but I did not find --vcf-half-call option in this command.

BTW, the version of the LDBlockShow I used is 1.40. I have 74915 phased SNV from 32 samples.

My command is as follows

LDBlockShow -InVCF final.snv.alt.vcf.gz -OutPut ./this_snv_LD -Region chr10:65726063-73410226

Thanks!

hewm2008 commented 2 years ago

Dear @PengJia6 I think some format of VCF file.

if your vcf format is haploid vcf format, I suggest to make some changes. haploid ---》 Diploid you should change the GT "0" ---> "0|0" or "0/0" "1" ---> "1|1" or "1/1" In theory, the data of the haploid ---> diploid VCF data, which does not affect the change of Decay. https://github.com/BGI-shenzhen/PopLDdecay/issues/7

also you can send me your data to my email, I try to run this for you.

PengJia6 commented 2 years ago

Thanks for your response!

My sample is diploid, I removed the record with missed GT, such as "./." or "./1", and it worked.

Thanks again! Peng

hewm2008 commented 2 years ago

Thanks for using the software. best wishes