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dnanexus-archive / parliament2

Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
Apache License 2.0
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svtyper throws exception on cnvnator vcf #37

Open scalavision opened 5 years ago

scalavision commented 5 years ago

When running svtyper on cnvnator.vcf I get this error:

Traceback (most recent call last):
  File "/usr/local/bin/svtyper", line 9, in <module>
    load_entry_point('svtyper==0.7.0', 'console_scripts', 'svtyper')()
  File "/usr/local/lib/python2.7/dist-packages/svtyper/classic.py", line 575, in cli
    sys.exit(main())
  File "/usr/local/lib/python2.7/dist-packages/svtyper/classic.py", line 568, in main
    args.max_ci_dist)
  File "/usr/local/lib/python2.7/dist-packages/svtyper/classic.py", line 265, in sv_genotype
    ciA = confidence_interval(var, 'CIPOS', 'CIPOS95', max_ci_dist)
  File "/usr/local/lib/python2.7/dist-packages/svtyper/parsers.py", line 12, in confidence_interval
    ci = map(int, var.info[tag].split(','))
KeyError: 'CIPOS'

Looking at this line and by investigating the python scripts being used, it seems like it should be the cvnator.ci.vcf file that should be the target of svtyper?

https://github.com/dnanexus/parliament2/blob/master/parliament2.sh#L471

The keys CIPOS and CIEND and several others are needed by svtyper and are not available in the original cnvnator.vcf file. This is according to this bug report in svtyper:

https://github.com/hall-lab/svtyper/issues/64

slzarate commented 5 years ago

Thank you for reporting this issue! I will look into this.