Open rajdbs32 opened 1 year ago
Hi, Sorry for the delay, Do you have a genotype GT in your sample column ? regarding the issue it seems to be that, don't forget to match metadata in the header too because PyVCF3 ( python lib which read vcf) take into account the dtype and some other informations,
Best,
JB
Hi,
Is there a way to run vcf2circos with VCF files that don't have GT field ? (I am working with vcf from NanomonSV which don't provide this information)
Thanks ! Tom
Hi, Unfortunately the only way to do so is to add a fictive genotype for all your variants, Simply add FORMAT column with GT and Sample column with 0/1 on all variants,
Best,
Jean-Baptiste
I generated vcf's from MANTA then annotated them using AnnotSV tool. then tried running vcf2circos tool i get this error :
Traceback (most recent call last): File "/home/genomics/anaconda3/envs/circos/bin/vcf2circos", line 8, in
sys.exit(main())
File "/mnt/data/circos/vcf2circos-master/vcf2circos/main.py", line 119, in main
js = Datafactory(input_file, options).plot_dict()
File "/mnt/data/circos/vcf2circos-master/vcf2circos/datafactory.py", line 25, in plot_dict
pc = Plotconfig(
File "/mnt/data/circos/vcf2circos-master/vcf2circos/plotcategories/plotconfig.py", line 100, in init
self.data = self.process_vcf()
File "/mnt/data/circos/vcf2circos-master/vcf2circos/utils.py", line 481, in timeit_wrapper
result = func(*args, **kwargs)
File "/mnt/data/circos/vcf2circos-master/vcf2circos/plotcategories/plotconfig.py", line 157, in process_vcf
if self.get_copynumber_type(record)[0] in ["BND"]:
File "/mnt/data/circos/vcf2circos-master/vcf2circos/plotcategories/plotconfig.py", line 247, in get_copynumber_type
self.get_copynumber_values(cast_svtype(svtype), record),
File "/mnt/data/circos/vcf2circos-master/vcf2circos/plotcategories/plotconfig.py", line 300, in get_copynumber_values
genotype = record.samples[0].data.GT
AttributeError: 'CallData' object has no attribute 'GT'
this is how my vcf looks