bcftools fails to index VCF with extra trailing new line #45

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winni2k opened this issue May 7, 2014 · 1 comment

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winni2k commented May 7, 2014

Hi,
I tried indexing the bgzipped example VCF from the bioperl project found at http://www.well.ox.ac.uk/~winni/outgoing/example.vcf.gz and I get the following error:

$ bcftools index example.vcf.gz
[E::get_intv] failed to parse TBX_VCF, was wrong -p [type] used?

[E::hts_idx_push] unsorted positions

When I remove the trailing new line the error disapears. Is this a bug?

The text was updated successfully, but these errors were encountered:

Member

pd3 commented May 7, 2014

Hi,
no, this is not a bug. The VCF is broken, empty lines are not allowed.

pd3 closed this as completed

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