bcftools view will not read VCF file

Question: bcftools view will not read VCF file

2.2 years ago by

patterh • 20 wrote:

Hi,

BCFtools view allows the reversible conversion between BCF and VCF formats. In Galaxy the default input is BCF format, but the input type can be changed by selecting "yes" at the "The input is VCF instead of BCF" dropdown listbox. However, even with VCF input selected, the items selectable from the history remain only BCF format files, and not VCF format files. Is this a quirk with BCFtools on Galaxy?

Thanks,

bfctools bcf software quirk vcf input • 1.1k views

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modified 2.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.2 years ago by patterh • 20

Hello,

First double check that the input datasets have "vcf" assigned as the datatype metadata. This is how: https://wiki.galaxyproject.org/Support#Tool_doesn.27t_recognize_dataset

I am also going in to run a test to see if the tool itself has some new issue. More feedback once that is done.

Thanks for reporting the problem, Jen, Galaxy team

ADD REPLY • link written 2.2 years ago by Jennifer Hillman Jackson ♦ 25k

2.2 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

I can confirm the issue. I am not sure if this option is even appropriate for this particular wrapper of the underlying tool - but will follow up on that. If it is, the option needs to be tuned and probably moved up the tool form to be closer to the input selection. At a minimum, the option should either work or be removed.

Changes (if any) would take a while to implement. I suggest skipping this tool. Use the tools in VCF Manipulation to work with VFC datasets instead.

Thanks again, Jen, Galaxy team

ADD COMMENT • link modified 2.2 years ago • written 2.2 years ago by Jennifer Hillman Jackson ♦ 25k

Update: I contacted the tool author about the issue to let him decide how this would be best resolved. Thanks! Jen

ADD REPLY • link written 2.2 years ago by Jennifer Hillman Jackson ♦ 25k

Thanks Jen! Appreciated.

Kind regards,

Hugh

ADD REPLY • link written 2.2 years ago by patterh • 20

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