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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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Why it went wrong? #22

Closed janking1 closed 2 years ago

janking1 commented 2 years ago

My code was shown below: ./LDBlockShow -InPlink 1557_indifreq_cal_pc1_more_equ_0_1557_indi -Region 4:72694947-7869226 -OutPut 1557_indifreq_cal_pc1_more_equ_0_1557_indi -OutPdf ;But I come across the message like "Error: Invalid .bed file size (expected 3147663 bytes)". I checked my data and I find the expected size was the same as my data, how can I solve this problem? It would be great if I receive your reply soon.

janking1 commented 2 years ago

sorry about that.I solve this problem already, turns out it came from the way I modified my sample ID

hewm2008 commented 2 years ago

your region give wrong :chr start end no chr end end 72694947 > 7869226 7869226* ?
you can try: ./LDBlockShow -InPlink 1557_indifreq_cal_pc1_more_equ_0_1557_indi -Region 4:72694947-78692260 -OutPut 1557_indifreq_cal_pc1_more_equ_0_1557_indi -OutPdf -OutPng

plink -file 1557_indifreq_cal_pc1_more_equ_0_1557_indi --allow-extra-chr --export vcf --out Region.vcf --chr 4 --from-bp 72694947 --to-bp 78692260

janking1 commented 2 years ago

thanks,that work!

At 2022-04-18 18:00:46, "hewm2008" @.***> wrote:

you region give wrong :chr start end no chr end end 72694947 > 7869226 7869226* ? you can try: ./LDBlockShow -InPlink 1557_indifreq_cal_pc1_more_equ_0_1557_indi -Region 4:72694947-78692260 -OutPut 1557_indifreq_cal_pc1_more_equ_0_1557_indi -OutPdf -OutPng

plink -file 1557_indifreq_cal_pc1_more_equ_0_1557_indi --allow-extra-chr --export vcf --out Region.vcf --chr 4 --from-bp 72694947 --to-bp 78692260

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