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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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InPut Para -Region chromosome [contig] can't be found in the SNP dataset #44

Open Jokendo-collab opened 3 weeks ago

Jokendo-collab commented 3 weeks ago

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.
hewm2008 commented 3 weeks ago

It is recommended that you change the chr name in your vcf from contig-0030316_TU to contig_0030316TU. gzip -d *vcf.gz ; sed -i '/contig-/contig/g' *.vcf

Jokendo-collab commented 3 weeks ago

This suggestion worked after changing the names. I also changed the contig names in my GFF file but when I pass my gff file I do not get gene names highlihted on my plot. I used the following command ./LDBlockShow-1.40/bin/LDBlockShow -InVCF merged_top_contigs.vcf -OutPut out_wik -Region contig_0023241_WIK:405598-14885150 -OutPng -InGFF top_contigs.gff out_wik

A snapshot of my GFF

##gff-version 3
# gffread v0.12.7
# gffread top_contigs.gtf -o output.gff
contig_0000620_WIK      Liftoff transcript      11183   86797   .       -       .       ID=ENSDART00000141197;geneID=ENSDARG00000093410;gene_name=BX936421.1
contig_0000620_WIK      Liftoff exon    11183   11329   .       -       .       Parent=ENSDART00000141197
contig_0000620_WIK      Liftoff exon    19485   19606   .       -       .       Parent=ENSDART00000141197
contig_0000620_WIK      Liftoff exon    85346   85563   .       -       .       Parent=ENSDART00000141197
contig_0000620_WIK      Liftoff exon    86736   86797   .       -       .       Parent=ENSDART00000141197
contig_0000620_WIK      Liftoff transcript      17901   18413   .       +       .       ID=ENSDART00000145203;geneID=ENSDARG00000094881;gene_name=si:ch211-197h24.8
contig_0000620_WIK      Liftoff exon    17901   18413   .       +       .       Parent=ENSDART00000145203
contig_0000620_WIK      Liftoff transcript      211435  272337  .       +       .       ID=ENSDART00000002428;geneID=ENSDARG00000011188;gene_name=acvr2aa
contig_0000620_WIK      Liftoff exon    211435  212486  .       +       .       Parent=ENSDART00000002428
contig_0000620_WIK      Liftoff exon    230143  230353  .       +       .       Parent=ENSDART00000002428
contig_0000620_WIK      Liftoff exon    236218  236327  .       +       .       Parent=ENSDART00000002428
contig_0000620_WIK      Liftoff exon    246778  246932  .       +       .       Parent=ENSDART00000002428
contig_0000620_WIK      Liftoff exon    262440  262583  .       +       .       Parent=ENSDART00000002428
contig_0000620_WIK      Liftoff exon    264804  264947  .       +       .       Parent=ENSDART00000002428
contig_0000620_WIK      Liftoff exon    265567  265712  .       +       .       Parent=ENSDART00000002428
contig_0000620_WIK      Liftoff exon    267272  267386  .       +       .       Parent=ENSDART00000002428
contig_0000620_WIK      Liftoff exon    268198  268336  .       +       .       Parent=ENSDART00000002428
contig_0000620_WIK      Liftoff exon    270727  270857  .       +       .       Parent=ENSDART00000002428
contig_0000620_WIK      Liftoff exon    270939  272337  .       +       .       Parent=ENSDART00000002428
contig_0000620_WIK      Liftoff CDS     212432  212486  .       +       0       Parent=ENSDART00000002428
contig_0000620_WIK      Liftoff CDS     230143  230353  .       +       2       Parent=ENSDART00000002428
contig_0000620_WIK      Liftoff CDS     236218  236327  .       +       1       Parent=ENSDART00000002428
contig_0000620_WIK      Liftoff CDS     246778  246932  .       +       2       Parent=ENSDART00000002428
contig_0000620_WIK      Liftoff CDS     262440  262583  .       +       0       Parent=ENSDART00000002428
contig_0000620_WIK      Liftoff CDS     264804  264947  .       +       0       Parent=ENSDART00000002428
contig_0000620_WIK      Liftoff CDS     265567  265712  .       +       0       Parent=ENSDART00000002428
contig_0000620_WIK      Liftoff CDS     267272  267386  .       +       1       Parent=ENSDART00000002428
contig_0000620_WIK      Liftoff CDS     268198  268336  .       +       0       Parent=ENSDART00000002428
contig_0000620_WIK      Liftoff CDS     270727  270857  .       +       2       Parent=ENSDART00000002428
contig_0000620_WIK      Liftoff CDS     270939  271133  .       +       0       Parent=ENSDART00000002428
hewm2008 commented 3 weeks ago

Because the region you gave is too large, so the gene length is too small and it looks like just a solid line when drawn, so by default, genes with more than 30 are not drawn. You can adjust this parameter ./ShowLDSVG -GeneLimtNum 100

./LDBlockShow-1.40/bin/ShowLDSVG -InPreFix out_wik -OutPng -InGFF top_contigs.gff -GeneLimtNum 100 -OutPut outFig