I used LDBlockShow to analysis my vcf file. But I can't get any output.

[GuLinLin-JMU]

Hi,

I used LDBlockShow to analysis my vcf file. But I can't get any output.

Start Time : Tue Mar 1 16:37:37 CST 2022

warning skip Indel site, there are total skip Indel sites number is : 1

Warning skip low Minor Allele Frequency site, and total skip allelic sites number is :103

Start Region Cal... :19 44889596 45932557; In This Region TotalSNP Number is 130

Start draw... SVG info: SNPNumber :130 , SVG (width,height) = (4485,4797) In Big SNP Number :130 ,Para -NumGradien suggest be maxValue : 32 ,auto be it Argument "" isn't numeric in log at /mnt/data9/gulinlin/biosoft/LDBlockShow-master/bin///ShowLDSVG line 992. Can't take log of 0 at /mnt/data9/gulinlin/biosoft/LDBlockShow-master/bin///ShowLDSVG line 992. Tip: The region you inputed is greater than the Para [-NoShowLDist], and this will call LDheatmap to be a not-complete triangle. You can modify the parameter [-NoShowLDist] according to your needs. find blocks... Start draw... SVG info: SNPNumber :130 , SVG (width,height) = (4485,4797) Argument "" isn't numeric in log at /mnt/data9/gulinlin/biosoft/LDBlockShow-master/bin//ShowLDSVG line 992. Can't take log of 0 at /mnt/data9/gulinlin/biosoft/LDBlockShow-master/bin//ShowLDSVG line 992. End Time : Tue Mar 1 16:39:26 CST 2022

My command is as follows $LDBlockShow_dir/LDBlockShow -InPlink sample -OutPut ./Lipoprotein_A_imputed/Lipoprotein_A_imputed_chr19 -Region 19:44889596:45932557 -InGWAS Lipoprotein_A_imputed.pvalue -SeleVar 2 -OutPng
$LDBlockShow_dir/ShowLDSVG -InPreFix ./Lipoprotein_A_imputed/Lipoprotein_A_imputed_chr19 -OutPut out_chr19 -InGWAS Lipoprotein_A_imputed.pvalue -NoShowLDist 20000000 -Cutline 6.913226 -PointSize 1 -NumGradien 32 -OutPng Thanks!

[hewm2008]

the chr name of gwas file and vcf file should be the same . please check it . The input chr name should be the same with the VCF files . also the chr name of gwas file should be the same .

[GuLinLin-JMU]

Thanks for your response! I have a new problem. Start Time : Fri Mar 4 11:13:22 CST 2022

warning skip Indel site, there are total skip Indel sites number is : 2

Warning skip low Minor Allele Frequency site, and total skip allelic sites number is :324

Start Region Cal... :2 232482038 236228699; In This Region TotalSNP Number is 469

find blocks... In Big SNP Number :469 ,Para -NumGradien suggest be maxValue : 32 ,auto be it Start draw... SVG info: SNPNumber :469 , SVG (width,height) = (5393.5,5768.7) Tip: The region you inputed is greater than the Para [-NoShowLDist], and this will call LDheatmap to be a not-complete triangle. You can modify the parameter [-NoShowLDist] according to your needs. Can't take log of 0 at /mnt/data9/gulinlin/biosoft/LDBlockShow-master/bin///ShowLDSVG line 989. In Big SNP Number :469 ,Para -NumGradien suggest be maxValue : 32 ,auto be it Start draw... SVG info: SNPNumber :469 , SVG (width,height) = (5393.5,5768.7) Can't take log of 0 at /mnt/data9/gulinlin/biosoft/LDBlockShow-master/bin//ShowLDSVG line 989. End Time : Fri Mar 4 11:22:25 CST 2022 Thanks!

[hewm2008]

code line 989 is : $hashPvalue{$key}=0-((log($hashPvalue{$key}))/log(10));

so I thinks in this region(:2 232482038 236228699) the may some gwas pvalue be exists 0 , you can awk this region gwas.pvalue. and check it at your GwasPvalue.file A: you can awk this region gwas.palvue. and check it cat GwasPvalue.file | awk '$1 ==2 && $2 >=232482038 && $2< 236228699'

B ：

I think it may be the effect of the line end of different systems. you can execute the following command dos2unix GwasPvalue.file