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hall-lab / svtools

Tools for processing and analyzing structural variants.
MIT License
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Not able to convert vcf to bedpe (Manta output) #322

Open Giuseppe1995 opened 2 years ago

Giuseppe1995 commented 2 years ago

Hi! I am trying to convert a Manta-called VCF structural variants file to bedpe format. here the code I use

svtools vcftobedpe -i somaticSV.vcf -o myFile.bedpe

and there the error I get (I can't program in Python)

Traceback (most recent call last): File "/srv/ngsdata/dalteriog/Tools/miniconda3/envs/ngspipe/bin/vcftobedpe", line 503, in sys.exit(main()) File "/srv/ngsdata/dalteriog/Tools/miniconda3/envs/ngspipe/bin/vcftobedpe", line 498, in main vcfToBedpe(args.input, args.output,args.confidence) File "/srv/ngsdata/dalteriog/Tools/miniconda3/envs/ngspipe/bin/vcftobedpe", line 371, in vcfToBedpe vcf.add_header(header) File "/srv/ngsdata/dalteriog/Tools/miniconda3/envs/ngspipe/bin/vcftobedpe", line 68, in add_header self.add_format(*[b.split('=')[1] for b in r.findall(a)]) IndexError: list index out of range

I downloaded svtools with conda

I'Ve looked up in the issue of this page, and apparently I made everything was needed to Can you tell me where am I mistaking?

Giuseppe