support for haploid genomes? about grenepipe HOT 8 CLOSED

Aha, thanks. Trying now, will report back. BTW, I think you have the links for HaplotypeCaller and BaseRecalibrator swapped in the comments

from grenepipe.

Hi @bensprung,

the extra params for each tool in the config file are meant for this purpose. That being said, I have not tested the pipeline with any non-diploid species, so I'd be curious to hear your feedback! I think it should work, as long as you specify ploidy for all tools that require it to be set.

Let me know if this works for you ;-)
Lucas

from grenepipe.

Hi Lucas I knew I was missing something simple, thanks.

I'm a little confused about one thing, would I make a new line that is

HaplotypeCaller-ploidy: 1

or

ploidy: 1

from grenepipe.

Hi @bensprung,

the types of entries/lines in the config file are pre-defined by the pipeline, and it is looking for specific keys. So, adding a new key that is not used by grenepipe would not have any effect at all.

What you want to do instead is fill in the values as needed. In your case, you want to change the line

HaplotypeCaller: ""

to

HaplotypeCaller: "-ploidy 1"

That is, within the quotation marks, you give the exact arguments that you want, as if you were calling GATK HaplotypeCaller yourself from the command line.

Let me know if this works ;-)

from grenepipe.

So it seems to work find with "-ploidy 1" passed along. No more pesky 0|1's!

from grenepipe.

Awesome! And none of the downstream tools complained about this? I'm closing this issue then - but feel free to re-open if needed :-)

Also, thanks for hint about swapped links!

from grenepipe.

Apparently not, at least the snpeff output looks like it makes sense so far.

from grenepipe.

Perfect, glad to hear :-)

from grenepipe.