Hello,
I have not find size options related to labels, how can I edit or add font size codes?
Thanks

Hi,

I have tried with several different things but I get these error messages:
aWrining: SVG module in Perl is missing, trying to loading the built-in [SVG.pm]...
Loading SVG module done
Start draw... SVG info: SNPNumber :0 , SVG (width,height) = (0,0)
Use of uninitialized value in subtraction (-) at /Users/kajsabrolin/Desktop/LDBlockShow-1.38/bin//ShowLDSVG line 564, line 1.
Use of uninitialized value in subtraction (-) at /Users/kajsabrolin/Desktop/LDBlockShow-1.38/bin//ShowLDSVG line 564, line 1.
Use of uninitialized value in subtraction (-) at /Users/kajsabrolin/Desktop/LDBlockShow-1.38/bin//ShowLDSVG line 586, line 1.
Use of uninitialized value in subtraction (-) at /Users/kajsabrolin/Desktop/LDBlockShow-1.38/bin//ShowLDSVG line 586, line 1.
Illegal division by zero at /Users/kajsabrolin/Desktop/LDBlockShow-1.38/bin//ShowLDSVG line 586, line 1.

Could you help me with this? Thanks!

I am getting the above error even though the region is present in my data. What could be wrong?

./LDBlockShow-1.40/bin/LDBlockShow -InVCF haplotype_gene_quantification/g3_variants/haptags_rna_variants/variant_calling/merged_top_contigs.vcf.gz -r contig-0030316_TU:10009058-10058862 -OutPut testLD 
		InPut Para -Region  chromosome [contig]  can't be found in the SNP dataset
Start draw... SVG info: SNPNumber :0 , SVG (width,height) = (0,0)
Use of uninitialized value in subtraction (-) at rna_sequences/haplotype_gene_quantification/LDBlockShow-1.40/bin//ShowLDSVG line 545, <IB> line 1.
Use of uninitialized value in subtraction (-) at rna_sequences/haplotype_gene_quantification/LDBlockShow-1.40/bin//ShowLDSVG line 545, <IB> line 1.
Use of uninitialized value in subtraction (-) at rna_sequences/haplotype_gene_quantification/LDBlockShow-1.40/bin//ShowLDSVG line 572, <IB> line 1.
Use of uninitialized value in subtraction (-) at rna_sequences/haplotype_gene_quantification/LDBlockShow-1.40/bin//ShowLDSVG line 572, <IB> line 1.
Illegal division by zero at rna_sequences/haplotype_gene_quantification/LDBlockShow-1.40/bin//ShowLDSVG line 572, <IB> line 1.

Dear developer,

I am new to using packages and tools.

First of all, thank you for this tool. It looks simple. But, I couldn't get any expected outputs after trying many attempts as much as I could. When I used test files from Example folder, I can get as recommended. But with my file, always showed the following message in that attached image.

Please check and help me with this problem.

thanks,

Dear friends,

Do you know how to increase the quality (resolution) of this output image?

Thank you very much,

Hu

@hewm2008 hello, I have some trouble with this tool. when I use the following code, it always return to a error. Thank you for your help.

$ LDBlockShow -InVCF thal_qc_4.vcf.gz -Region 1:28400000:29400000 -OutPdf -OutPut chr1:28968982_C/A

open OUT File error: chr1:28968982_C/A.region.vcf

less -S chr1:28968982_C/A.region.vcf
##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20231221
##source=PLINKv1.90
##contig=<ID=1,length=248945580>
##contig=<ID=2,length=242180055>
##contig=<ID=3,length=198109145>
##contig=<ID=4,length=190203754>
##contig=<ID=5,length=181362783>
##contig=<ID=6,length=170742179>
##contig=<ID=7,length=159334897>
##contig=<ID=8,length=145075237>
##contig=<ID=9,length=138318532>
##contig=<ID=10,length=133767313>
##contig=<ID=11,length=135076488>
##contig=<ID=12,length=133264228>
##contig=<ID=13,length=114353269>
##contig=<ID=14,length=106883602>
##contig=<ID=15,length=101980932>
##contig=<ID=16,length=90215708>
##contig=<ID=17,length=83231328>
##contig=<ID=18,length=80262556>
##contig=<ID=19,length=58606454>
##contig=<ID=20,length=64329662>
##contig=<ID=21,length=46699694>
##contig=<ID=22,length=50801121>
##INFO=<ID=PR,Number=0,Type=Flag,Description="Provisional reference allele, may not be based on real reference genome">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##bcftools_viewVersion=1.17+htslib-1.17
##bcftools_viewCommand=view -r chr1:28400000-29400000 -o chr1_28968982_C_A.vcf thal_qc_4.vcf.gz; Date=Sat Dec 23 21:47:30 2023
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ....

Hi!
I use Plink to convert the my vcf format，but I encountered the following problems:

Error: Line 28 of .vcf file has a GT half-call.
Use --vcf-half-call to specify how these should be processed.

But I didn't find --vcf-half-call.

Error: Missing --vcf-half-call parameter.
For more information, try "plink --help " or "plink --help | more".

My command is :
plink --vcf PT8.vcf --recode HV --out pap.region.hv --allow-extra-chr

Thanks!

I use conda install -c bioconda ldblockshow ,but ShowLDSVG is not working,so can you help me ?
BEGIN failed--compilation aborted at /bin/ShowLDSVG line 24.

Hello,

Thanks for developing LDblock show! I see the default colors for SNPs in the regional Manhattan plots are blue for insignificant SNPs and red for signifcant ones. Is it possible to change those colors? I don't see an option to do so in the manual but i've seen LDBlockShow-generated figures in manuscripts with different colors than the default.

Thanks a lot for any help with this,
Elissa

Hi, I used the sample file and a Segmentation fault occurred. I'm using Ubuntu 20.04.5 LTS from WSL, and I don't know if you have a fix. Thank you, sir.
./LDBlockShow -InVCF ../example/Example1/Test.vcf.gz -OutPut out -Region chr11:24000000:24400000 -OutPng -SeleVar 2

#Detected VCF File is phased file with '|', Read VCF in Phase mode
#Warning skip low Minor Allele Frequency site, and total skip allelic sites number is :11
##Start Region Cal... :chr11 24000000 24400000; In This Region TotalSNP Number is 7
find blocks...
Segmentation fault
mv: cannot stat 'out.plink.blocks.det': No such file or directory
gzip: out.blocks: No such file or directory
Warining: SVG module in Perl is missing, trying to loading the built-in [SVG.pm]...
Loading SVG module done
Start draw... SVG info: SNPNumber :7 , SVG (width,height) = (455,385)
convert SVG ---> PNG ...
ALL done

./LDBlockShow -InVCF ../Example1/Test.vcf.gz -OutPut out -Region chr11:24100000:24200000 -InGWAS ../Example2/gwas.pvalue -SeleVar 2
Segmentation fault

Hello,

When use LDBlockShow to non-human genome, how to set the chromosome set?

Thanks in avance!

C

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!

Hi He,

I found one question that the SVG size could not be adjusted by -ResizeH function, I used the command line in the attachment and got a partial plot (please see the bottom of the plot). Please check the attachment for details, thanks a lot for your continuous helps.

Best regards,

Hu

Thanks for this new tool!

I found the pre-print for LDBlockShow on the biorxiv. Since LDBlockShow is distributed under an open license (MIT), I added a package recipe so it will be available via the bioconda channel of the conda package manager. I hope that's ok! This makes it easy to install via a simple command:

conda install -c bioconda ldblockshow

It looks like there have already been some downloads of LDBlockShow from bioconda: https://anaconda.org/bioconda/LDblockshow

If changes should be made to the LDBlockShow recipe, please let me know or feel free to open pull requests to the bioconda-recipes repository. We welcome contributions!
(more info on contributing to bioconda here: https://bioconda.github.io/contributor/index.html )

Hello! I have been having a fun time learning how to use your program. I am trying to make a pairwise plot for specific SNP's in the ABO gene on chromosome 9. So far I've been able to make the pairwise plot for the entire gene region which includes many polymorphisms. I used the -SepSNPName command to highlight my specific SNPS. Is there any way that I can just use these specific SNPS to make the plot instead of including every polymorphism within my selected region?

hi, LDBlockShow,

when i run the software, i got the tips:

/##Start Region Cal... :4 27920799 28120799; In This Region TotalSNP Number is 815
find blocks...
Warining: SVG module in Perl is missing, trying to loading the built-in [SVG.pm]...
Loading SVG module done
In Big SNP Number :815 ,Para -NumGradien suggest be maxValue : 20 ,auto be it
Start draw... SVG info: SNPNumber :815 , SVG (width,height) = (4686.25,5012.25)
Argument "" isn't numeric in log at /home/liling/software/LDBlockShow/bin/ShowLDSVG line 999.
Can't take log of 0 at /home/liling/software/LDBlockShow/bin/ShowLDSVG line 999.

I have seen the previous related issues, and i checked my file and argument, but 1) no 0 in my pvalue row. 2) my file is't upload from windows system. 3) I changed my P-value (e.g 9.9E-01 to 9.9e-01) but doesn't work.
It is strange that it is work well when I analyze another region using same file.
Do you have any suggestions?

my GwasPvalue:
........
9 290382128 9.9999473386657933e-01
8 266898947 9.9999495277533279e-01
8 266900669 9.9999495277533279e-01
11 344518005 9.9999630054136868e-01
6 193914078 9.9999661058091205e-01
11 339891177 9.9999732210144965e-01
4 143133024 9.9999747570906627e-01
2 52265629 9.9999933256549600e-01
12 359378455 9.9999958203621164e-01
4 135004607 9.9999984697910282e-01
..........

I install LDBlockShow by conda.
After installed, I test by --help, It is all right.
But when I execute with input vcf files , it failed.
Code as follow:

source ~/software/anaconda3/bin/activate
conda activate ldblockshow
vcf=4017_chr12_common_aa.vcf.gz
LDBlockShow -InVCF ${vcf} \
            -OutPut ALDH2_LD \
            -Region 12:111303962:112303962 \
            -SeleVar 2

failed as follow:

What's the problem?

Hello,
I have a large vcf (27 chromosomes (2.5Gb), 96 diploid samples, and >18 million SNPs) and I have done a fair amount of pre-filtering. I am testing LDBlockShow on our smallest chromosome (18Mb and >500,000 SNPs).

I ran:

LDBlockShow -InVCF Chr26_2pops_HW.vcf.gz -OutPut out -Region Chr26_nm_RagTag:1:18055847 -OutPng -SeleVar 2

I am getting the following warning and no command line prompt after 3 hours.

#Warning skip non bi-allelic(Singleton/ThreeMulti allelic) site, and total skip allelic sites number is :28792
#Warning skip high missing site, and total skip allelic sites number is :43138
#Warning skip low Minor Allele Frequency site, and total skip allelic sites number is :212107
##Start Region Cal...    :Chr26_nm_RagTag 1 18055847; In This Region TotalSNP Number is 239684
Warning: LDBlocks Region SNP Number too much, you may use the small region or more stringent conditions to filter the SNP

I can see from running 'top' that LDBlockShow is running and only using a single thread. I have two questions:

1. Should the process abort on these warnings? or is it going to complete its run and provide output files?
2. Is there a way to use multiple threads? I have 256 threads and 2 TB RAM.

Hi,
I have located a range in VCF file with eight snp number, but the LDBlockShow did not detect these SNP numbers and said there is no snp markers among the range I defined. do you know the reason why?

Thanks a lot for your help.

Hu

Hi @hewm2008 ,
I'd drawm a svg graph with a range of 1.5 Mb contig and more than 10k bi-allelic snps. While the program report an error like this:

So how could I select the height value? Otherwise, a large chart convert program may need large memory , so how many memory should I to select in the perl script svg2xxx.pl? Thanks in anvances.

Best Regards,
Yung-Chien

您好 @hewm2008 ，
我在做一个大约长1.5Mb的ld Block分析，其中包含了10k多的bi-allelic snps。这种分析首先产生了这样的一个错误：

我该如何选择Height参数呢？此外，由于svg转png这一步会消耗大量内存，设置一个低ppi的话会不会缩短运行时间以及节省内存呢？谢谢您。
祝好，
Yung-Chien

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

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.

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!

Dear friends,
Thank you for the good software. When I tried this software for the first time, it shows the problem as follows,
command line: ./LDBlockShow -InVCF est_vcf.vcf -OutPut gd -InGWAS GWASpvalue.txt -InGFF LDBlockShow/Bos_taurus.ARS-UCD1.2.103.gff3.gz -Region 11:24000000:24200000 -OutPng -SeleVar 3
##Start Region Cal... :11 24000000 24200000; In This Region TotalSNP Number is 7
find blocks...
Start draw... SVG info: SNPNumber :7 , SVG (width,height) = (455,518)
Argument "" isn't numeric in log at /LDBlockShow/bin//ShowLDSVG line 999.
Can't take log of 0 at /LDBlockShow/bin//ShowLDSVG line 999.

I try to find the reason, but it no success. Could you please give me some advice on that?
Best,
fruce

$ LDBlockShow -InVCF 507sample.vcf_Chr_id.vcf -OutPut file -Region chr14:55370544:55870544 -OutPng
#Detected VCF File is phased file with '|', Read VCF in Phase mode
InPut Para -Region chromosome [chr14] can't be found in the SNP dataset
Warining: SVG module in Perl is missing, trying to loading the built-in [SVG.pm]...
Loading SVG module done
Start draw... SVG info: SNPNumber :0 , SVG (width,height) = (0,0)
Use of uninitialized value in subtraction (-) at /public/home/yplu/biosoft/LDBlockShow-1.36/bin//ShowLDSVG line 510, line 1.
Use of uninitialized value in subtraction (-) at /public/home/yplu/biosoft/LDBlockShow-1.36/bin//ShowLDSVG line 510, line 1.
Use of uninitialized value in subtraction (-) at /public/home/yplu/biosoft/LDBlockShow-1.36/bin//ShowLDSVG line 532, line 1.
Use of uninitialized value in subtraction (-) at /public/home/yplu/biosoft/LDBlockShow-1.36/bin//ShowLDSVG line 532, line 1.
Illegal division by zero at /public/home/yplu/biosoft/LDBlockShow-1.36/bin//ShowLDSVG line 532, line 1.

I was just wanting to clarify how the r^2 values in the triangle output correspond to specific pairs of snps. Is the first row and first column element the r^2 of the snps of the first and last positions? The first column and last row element is the r^2 value corresponding to the first and second snp? The last column and first row element is the r^2 of the last and second to last snp?

Thanks

Hi,
I am working on the plant genome and I am interested in finding the haplotype blocks in my whole chromosome. Is it okay, if I put the coordinates of whole chromosomes for finding the haplotype blocks and then visualize the specific blocks?

Also, I am curious about how to define the haplotype blocks in the output.

Thank you in advance
Megha Sharma

Hello,

Could you help me solve the "-NoLogP" code by any chance? it looks not working.

for example,

../bin/LDBlockShow -InVCF GWAS_Only_Chromosome_Biallelic.Filter_out.0.05MAF_50%Missing.vcf.gz -MAF 0.05 -Miss 0.6 -OutPut Chr2.4_58225679 -Region chr2.4:54758224-59306183 -SpeSNPName Chr2.4_58225679_spe.snp -InGWAS Chr2.4_58225679_gwas.pvalue -Cutline 5 -OutPng -SeleVar 1 -ShowNum -BlockType 3 -BlockCut 0.8 -NoLogP

I was trying to put -NoLogP at different positions, it still did not work.

Any help would be appreciated!

Hu

示例文件中GFF格式如下：

但是按参考文档里面说的GFF3格式文档格式是：

或者是

因此，不能显示出正确的gene名称
请问如何才能解决？或者如示例的GFF格式应该去哪里下载?
谢谢您

Hi there, I have two genotype data in PLINK format with the same BIM file and different FAM file, now I tried to compare the LD in two dataset without quality check, how can I do that in LDBlockShow?

Hello,

I've recently discovered this tool, and want to try it out on a large vcf.
I was wondering, is there any way to get LD analysis + plot across all chromosomes? I have chromosomes 1-18, and in addition to doing each chromosome alone, I would like to do analysis across all.

best
S

Hi LDBlockShow group,

I raised another question that do you have an example of gwas.pvalue format? Thanks a lot,

Hu

Hi,
I found some SNP/Indel sites were filtered, can I rescue them by certain parameters?
And I want to calculate LD of rare variants, setting "-MAF 0", but this parameter doesn't seem to work?
Please give me some guidance. Thank you！

Hi,

Do you know how to solve the overlapping SNP names in the plot? or How to stop the software to skip the high missing sites, why it is always skipping the highly missing sites, I already filter out the 50% missing genotypes and 5% MAF from my VCF file? (I believe this is the reason why SNP names are overlapping)

Please see the attachment

Thank you very much,

Hu

Hello every, I conduct the commend: LDBlockShow -InVCF aln_sorted2.vcf -OutPut out -Region NC_001802.1:1:2000 -OutPng -SeleVar 2
and got the result: #Warning skip non bi-allelic(Singleton/ThreeMulti allelic) site, and total skip allelic sites number is :15
##Start Region Cal... :NC_001802.1 1 2000; In This Region TotalSNP Number is 207
find blocks...
Warning: Skipping --blocks, since there are less than two founders with
nonmissing phenotypes. (--make-founders may come in handy here.)
mv: cannot stat ‘out.plink.blocks.det’: No such file or directory
gzip: out.blocks: No such file or directory
Can't locate SVG.pm in @inc

I don’t why I got this warnings. What information should we provide in the vcf file for LDBlockShow?

Thank you

Here is my error,it seems that this error comes from converting SVG 2 PNG, I have already install the "zlib 1.2.9" and using command "export LIBRARY_PATH=$LIBRARY_PATH:/WORK/scau_ljq_1/USER/szq/2022.4.15dsq_LD_haploview/lib" to set the path to "zlib 1.2.9", but it didn't work and shows the same error, I wonder is there somewhere I can truly set the path to "zlib 1.2.9":

system(paste0("./LDBlockShow ",

•           " -InPlink sub_snp_PLAG1_sub_eigen_expand_sig_3Mb_bonferroni_0.01_200k_1557_indi ",
  

•           " -Region 4:72694947:78692263 ",
  

•           " -OutPut ","sub_snp_PLAG1_sub_eigen_expand_sig_3Mb_bonferroni_0.01_200k_1557_indi ",
  

•           " -OutPng "
  

•           ))
  

#Warning skip low Minor Allele Frequency site, and total skip allelic sites number is :10303
##Start Region Cal... :4 72694947 78692263; In This Region TotalSNP Number is 7184
Start draw... SVG info: SNPNumber :7184 , SVG (width,height) = (6609.28,4885.12)
Too many SNP site 7184 , I suggest that you randomly select fewer sites to reshow , and here I try to draw ...
In Big SNP Number :7184 ,Para -NumGradien suggest be maxValue : 10 ,auto be it
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.
convert SVG ---> PNG ...
/usr/bin/convert: /WORK/app/anaconda3/5.3.0/lib/./libuuid.so.1: no version information available (required by /usr/lib64/libSM.so.6)
/usr/bin/convert: /WORK/app/zlib/1.2.8/lib/libz.so.1: version `ZLIB_1.2.9' not found (required by /WORK/app/anaconda3/5.3.0/lib/./libpng16.so.16)
ALL done
find blocks...

../../LDBlockShow/bin/LDBlockShow -InVCF chr3.sv.edited.filter.recode.vcf -OutPut hapl_block -Region 3:1-100000 -OutPng -SeleVar 1
#Warning skip non bi-allelic(Singleton/ThreeMulti allelic) site, and total skip allelic sites number is :20
#Warning skip low Minor Allele Frequency site, and total skip allelic sites number is :41
##Start Region Cal... :3 1 100000; In This Region TotalSNP Number is 34
find blocks...
Segmentation fault
mv: cannot stat 'hapl_block.plink.blocks.det': No such file or directory
gzip: hapl_block.blocks: No such file or directory
Warining: SVG module in Perl is missing, trying to loading the built-in [SVG.pm]...
Loading SVG module done
Start draw... SVG info: SNPNumber :34 , SVG (width,height) = (1955,1445)
convert SVG ---> PNG ...
ALL done

Hi,

I tried to run the LDBlockShow but it ran into the "8547 segmentation fault" and I'm not sure how to fix it, could you please check? Thanks!

➜ Ara_test git:(main) ✗ ../../bin/LDBlockShow -InVCF Ara_Ch4.vcf -OutPut out -Region chr4:920000:9240000 -OutPng
[1] 8547 segmentation fault ../../bin/LDBlockShow -InVCF Ara_Ch4.vcf -OutPut out -Region -OutPng

I attached here the head 50 of my vcf
50_Ara_Chr4.txt

LDBlockShow is an excellent tool, but ,

In the tutorial instruction (3.1.1 Main parameter), I would suggest a minor correction:

-Region, format should be chr:start:end, a prefix "chr" before the chromosome-interger should be unnecessary which depends on your chromosome variable format (chr1 or 1) in the vcf dataset.

Where it says:

3.1.1 Main parameter
./bin/LDBlockShow

    Usage: LDBlockShow  -InVCF  <in.vcf.gz>  -OutPut <outPrefix>  -Region  chr1:10000-20000

Details for above parameters:

 -Region         The defined region to show the LD heatmap (format: chr:start:end)

Reason:
"-Region chr11:24100000:24200000" indeed works fine with the example,
but more often in GWAS summary statistics, chromosome column, people use a single interger (i.e. 11) instead of format like chr11.
which is particularly true for 1000Genomes reference data and then:
"-Region 11:24100000:24200000" should be used to avoid warnings.

See also: https://www.internationalgenome.org/category/vcf/
Please note that all our VCF files using straight intergers and X/Y for their chromosome names in the Ensembl style rather than using chr1 in the UCSC style. If you request a subsection of a vcf file using a chromosome name in the style chrN as shown below it will not work.

Otherwise, you got warnings look like:

#Detected VCF File is phased file with '|', Read VCF in Phase mode
InPut Para -Region chromosome [chr16] can't be found in the SNP dataset

I ran across this problem and tried to fixed it with checking my query and "SNP datasets" for a whole day.
Only to find out the real problem was that I should not have followed the "format instruction" like "-Region chr16:169708:1169708"
Instead, just "-Region 16:169708:1169708" will work well.

Hi,

Thanks for this amazing and convenient tool,

I would like to ask one questions:

why the y axis label is -lg(Pvalue) rather than -log(Pvalue)?

Appreciate your help in advance!

[Lingchenjin@mu01 Example2]$ ../../bin/LDBlockShow -InVCF ../Example1/Test.vcf.gz -OutPut out -Region chr11:24100000:24200000 -InGWAS gwas.pvalue -OutPng -SeleVar 2
#Detected VCF File is phased file with '|', Read VCF in Phase mode
#Warning skip low Minor Allele Frequency site, and total skip allelic sites number is :11
##Start Region Cal... :chr11 24100000 24200000; In This Region TotalSNP Number is 7
find blocks...
sh: /home/Lingchenjin/LDBlookshow/LDBlockShow/example/Example2/../../bin/plink: Permission denied
mv: cannot stat ‘out.plink.blocks.det’: No such file or directory
gzip: out.blocks: No such file or directory
Warining: SVG module in Perl is missing, trying to loading the built-in [SVG.pm]...
Loading SVG module done
Start draw... SVG info: SNPNumber :7 , SVG (width,height) = (455,518)
convert SVG ---> PNG ...
Can't find the [ convert ] bin in your $PATH, I try to convert svg by /home/Lingchenjin/LDBlookshow/LDBlockShow/bin/svg_kit/svg2xxx.pl
Exception in thread "main" java.awt.AWTError: Can't connect to X11 window server using 'localhost:13.0' as the value of the DISPLAY variable.
at sun.awt.X11GraphicsEnvironment.initDisplay(Native Method)
at sun.awt.X11GraphicsEnvironment.access$200(X11GraphicsEnvironment.java:65)
at sun.awt.X11GraphicsEnvironment$1.run(X11GraphicsEnvironment.java:115)
at java.security.AccessController.doPrivileged(Native Method)
at sun.awt.X11GraphicsEnvironment.(X11GraphicsEnvironment.java:74)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:264)
at java.awt.GraphicsEnvironment.createGE(GraphicsEnvironment.java:103)
at java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(GraphicsEnvironment.java:82)
at java.awt.image.BufferedImage.createGraphics(BufferedImage.java:1181)
at org.apache.batik.ext.awt.image.GraphicsUtil.createGraphics(Unknown Source)
at org.apache.batik.gvt.filter.GraphicsNodeRed8Bit.genRect(Unknown Source)
at org.apache.batik.gvt.filter.GraphicsNodeRed8Bit.copyData(Unknown Source)
at org.apache.batik.ext.awt.image.rendered.TileCacheRed.genRect(Unknown Source)
at org.apache.batik.ext.awt.image.rendered.AbstractTiledRed.drawBlockInPlace(Unknown Source)
at org.apache.batik.ext.awt.image.rendered.AbstractTiledRed.drawBlock(Unknown Source)
at org.apache.batik.ext.awt.image.rendered.AbstractTiledRed.copyToRasterByBlocks(Unknown Source)
at org.apache.batik.ext.awt.image.rendered.AbstractTiledRed.copyData(Unknown Source)
at org.apache.batik.ext.awt.image.rendered.TranslateRed.copyData(Unknown Source)
at org.apache.batik.ext.awt.image.rendered.PadRed.copyData(Unknown Source)
at org.apache.batik.gvt.renderer.StaticRenderer.repaint(Unknown Source)
at org.apache.batik.gvt.renderer.StaticRenderer.repaint(Unknown Source)
at org.apache.batik.transcoder.image.ImageTranscoder.transcode(Unknown Source)
at org.apache.batik.transcoder.XMLAbstractTranscoder.transcode(Unknown Source)
at org.apache.batik.transcoder.SVGAbstractTranscoder.transcode(Unknown Source)
at org.apache.batik.apps.rasterizer.SVGConverter.transcode(Unknown Source)
at org.apache.batik.apps.rasterizer.SVGConverter.execute(Unknown Source)
at org.apache.batik.apps.rasterizer.Main.execute(Unknown Source)
at org.apache.batik.apps.rasterizer.Main.main(Unknown Source)
ALL done

When I use the example code " ../../bin/LDBlockShow -InVCF Test.vcf.gz -OutPut out1 -Region chr11:24100000:24200000 -OutPng -SeleVar 1 "
There is a error means"Can't find the [ convert ] bin in your $PATH, I try to convert svg by /home/weizian/LDBlockShow-1.40/bin/svg_kit/svg2xxx.pl "
What should I do to solve this problem.
Thank you!

Thanks for making and sharing this great tool.

I am trying to reproduce with plink the exact same D' prime values as observed in the TriangleV.gz file, using the following commands:

For LDBlockShow:

LDBlockShow -BlockType 1 -InVCF mydata.vcf.gz -OutPut output.ldblockshow -MAF 0.2

For PLINK:

vcftools --maf 0.2 VCF mydata.vcf.gz --gzvcf mydata.vcf.gz --recode --recode-INFO-all --out mydata.maf0.2

plink --vcf mydata.maf0.2.recode.vcf --allow-extra-chr --r2 dprime --ld-window 1000 --ld-window-kb 500 --ld-window-r2 0 --out output.plink

However, when I compare the first entries in the plink output and those in the TriangleV.gz file (assuming that the topleft values in the matrix correspond to the first lines in the plinkoutput.ld file), the values do not match. (In contrast, the haploblock regions identified with plink --blocks are identical).

Should I be using another plink command?

Thanks in advance for your help!

Menno