bndeval error

[Asher Bryant]

Hello -

I'm getting "Error: No VCF file format version header line found".  Both vcf files have "##fileformat=VCFv4.2", if that's relevant. 

The commands were:

SAVANA=$DIRECTORY/savana/sorted_colo829_tumor_xy.haplotagged.sv_breakpoints.vcf.gz

TRUTHSET=$DIRECTORY/colo829_truthset/vcfs/sorted_chr_truthset_somaticSVs_COLO829_hg38lifted.vcf.gz

rtg bndeval -b $TRUTHSET \

-c $SAVANA \

-o $DIRECTORY/bndeval_savana

Any help would be appreciated!

Best,

Asher

[Len Trigg]

Hi Asher,

My guess is that your VCF's are invalid in some way (e.g. perhaps they're actually uncompressed even though they have ".gz" extension). Check whether your VCF files can be read with rtg vcfstats. If you can't sort it out feel free to send through a small example and the exact command line you are using so we can replicate it here.

Cheers,

Len.

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