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hall-lab / svtyper

Bayesian genotyper for structural variants
MIT License
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svtyper on lumpy vcf #14

Closed lurens closed 9 years ago

lurens commented 9 years ago

hi I ran lumpy and got the vcf output file. I would like to run svtyper but i keep getting this error message: Traceback (most recent call last): File "./svtyper", line 1078, in sys.exit(main()) File "./svtyper", line 1070, in main args.debug) File "./svtyper", line 767, in sv_genotype sample = Sample(bam_list[i], spl_bam_list[i], num_samp) File "./svtyper", line 709, in init self.name = bam.header['RG'][0]['SM'] KeyError: 'RG'

Is it related to the -M issue? Thanks

cc2qe commented 9 years ago

probably not in this case. Do your BAM files have read groups? if not, i recommend https://github.com/ekg/bamaddrg to add them