Hi, after I import the bgz vcf file, the above command gives rise to the following error: FatalError: HailException: variant 10:32557367:CTTTTTTT:C,CT,CTT,CTTT,CTTTT: INFO field InbreedingCoeff: unable to convert -nan (of class java.lang.String) to Double: caught java.lang.NumberFormatException: …

-nan isn’t a valid string representation for a float, so that is causing problems. Where did this VCF come from?

vep annotated haplotype joint calling

Interesting – Python’s float('-nan') works but Java doesn’t support this. I’ll add a patch to support -nan from VCFs, but the patch is going into the 0.2 version, not 0.1. Can you switch?

not at the moment, besides the patch, other way I can rescue? Thanks.

you could probably change the VCF header line for that INFO field to type String.

copy the header of the VCF, edit it manually, then do import_vcf(['fake_header_file.vcf', 'real.vcf'])

make sure the modified header is first in the import_vcf file list.

we do really recommend switching to 0.2 as soon as possible, though!

my file is compressed version vcf.bfz…

Vds.summarize().report() error in hail 0.1

Help [0.1]

trptyrphe July 11, 2018, 2:46pm 7

You mean import_vcf step? how?

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Vds.summarize().report() error in hail 0.1

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