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eldariont / svim-asm

Structural Variant Identification Method using Genome Assemblies
GNU General Public License v3.0
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Multiple records in the same position #15

Open zhqduan opened 2 years ago

zhqduan commented 2 years ago

Hi,

I am using svim-asm to identify the SVs from haplotype-resovled human genomes. However, there are multiple records in the same position, with same length and genotype, a case showed as followed:

chr1 16565784 svim_asm.INS.259 C CT..CA . PASS SVTYPE=INS;END=16565784;SVLEN=1548 GT 1/1 chr1 16565784 svim_asm.INS.260 C CT..CA . PASS SVTYPE=INS;END=16565784;SVLEN=1580 GT 1/0 chr1 16565784 svim_asm.INS.261 C CT..CA . PASS SVTYPE=INS;END=16565784;SVLEN=6297 GT 1/1 chr1 16565784 svim_asm.INS.262 C CT...CA . PASS SVTYPE=INS;END=16565784;SVLEN=6297 GT 1/1 chr1 16565784 svim_asm.INS.263 C CT...CA . PASS SVTYPE=INS;END=16565784;SVLEN=10970 GT 0/1 chr1 16565784 svim_asm.INS.264 C CT...CA . PASS SVTYPE=INS;END=16565784;SVLEN=15719 GT 1/1

Could you explain that why it happened, and what should we do with this type SV. Thank you very much!

LuisGFdez commented 1 year ago

Hi, @zhqduan I have the same problem, Did u figure out how to solve it? or do you know why it happens?