svtools Genotype + Key Error: 'END'

[arumds]

I have used the svtools protocol at https://github.com/hall-lab/svtools/blob/master/Tutorial.md . However, i am having the below error while using svtools genotype:

Running svtyper with options: /svtools/bin/svtyper/svtyper --split_weight 1 -n 1000000 --disc_weight 1 -m 20 -B /wrk/proj/hWGS.sorted.bam -l /wrk/proj/recalibrated.bam.json Reading library metrics from /wrk/proj/recalibrated.bam.json... done Traceback (most recent call last): File "/svtools/bin/svtyper/svtyper", line 1768, in sys.exit(main()) File "/svtools/bin/svtyper/svtyper", line 1763, in main args.alignment_outpath) File "/svtools/bin/svtyper/svtyper", line 1480, in sv_genotype posB = int(var.get_info('END')) File "/svtools/bin/svtyper/svtyper", line 215, in get_info return self.info[field] KeyError: 'END' svtyper exited with code 1

Any tips to fix this are appreciated.

[ernfrid]

Your input VCF must have an END tag in the VCF for svtyper to work. If your input file is from svtools merge then I'd expect it to exist.