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PapenfussLab / StructuralVariantAnnotation

R package designed to simplify structural variant analysis
GNU General Public License v3.0
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Manta VCF: error in drawing circos plot #24

Closed TendoLiu closed 4 years ago

TendoLiu commented 4 years ago

Hi, I am currently using this package to draw a circos plot using a vcf file produced by Manta.

colo829_vcf <- VariantAnnotation::readVcf("Manta.vcf.gz") colo829_bpgr <- breakpointRanges(colo829_vcf) colo829_begr <- breakendRanges(colo829_vcf) suppressPackageStartupMessages(require(circlize)) colo829_bpgr_with_chr_prefix <- colo829_bpgr seqlevelsStyle(colo829_bpgr_with_chr_prefix) <- "UCSC" pairs <- breakpointgr2pairs(colo829_bpgr_with_chr_prefix) view(show(pairs)) circos.initializeWithIdeogram() circos.genomicLink(as.data.frame(S4Vectors::first(pairs)), as.data.frame(S4Vectors::second(pairs)))

Error in circos.genomicLink(as.data.frame(S4Vectors::first(pairs)), as.data.frame(S4Vectors::second(pairs))) : nrow of region1 and region2 differ.

Not sure where this message come from and how to solve it. Manta VCF file Manta.vcf.gz

d-cameron commented 4 years ago

Not an issue with StructuralVariantAnnotation. circos.genomicLink() strips your chr11_gl000202_random breakend (presumably because it's not in your circos reference).