Question: bcftools view will not read VCF file
2
gravatar for patterh
16 months ago by
patterh20
patterh20 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,

H

ADD COMMENTlink modified 16 months ago by Jennifer Hillman Jackson23k • written 16 months ago by patterh20

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 REPLYlink written 16 months ago by Jennifer Hillman Jackson23k
0
gravatar for Jennifer Hillman Jackson
16 months ago by
United States
Jennifer Hillman Jackson23k 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 COMMENTlink modified 16 months ago • written 16 months ago by Jennifer Hillman Jackson23k

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

ADD REPLYlink written 16 months ago by Jennifer Hillman Jackson23k

Thanks Jen! Appreciated.

Kind regards,

Hugh

ADD REPLYlink written 16 months ago by patterh20
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