Fixing phasing snps arguments and LiftOver

[oriolpich]

Dear Hatchet developers,
I spotted two issues when running the last version of Hatchet, and I suggest two solutions.

• The SNP argument when calling phase_snps() is swapped with the chromosome annotation and this causes an error. Sorting it properly fixest the issue.

• When installing Hatchet through conda, it also installs picard. This breaks the Liftover commands, which pressumably were using an old picard.jar file on your side. The fixes allowed Hatchet to move forward in the phasing bit.

Hope this helps.

Oriol

[vineetbansal]

Thanks @oriolpich. Just adding this here for reference once we get down to fixing it:
https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)

[vineetbansal]

@oriolpich - I might be mistaken but it looks to me like HATCHet is indeed using the newer syntax for picard (as per the link above). I just installed picard from bioconda and the HATCHet version of the command works just fine. HATCHet itself can deal with either the picard executable or a picard.jar.

Are you able to tell us where you installed picard from? If you can provide a version number that would be great too, so we can try to support both old and new versions of picard.

[oriolpich]

@vineetbansal I installed hatchet using conda, which installs picard as a dependency:

conda create -n hatch_picard -c bioconda hatchet

  picard             bioconda/noarch::picard-2.18.29-0

conda activate hatch_picard
~/.conda/envs/hatch_picard/bin/picard

picard LiftoverVcf 

Example

java -jar picard.jar LiftoverVcf \
I=input.vcf \
O=lifted_over.vcf \
CHAIN=b37tohg38.chain \
REJECT=rejected_variants.vcf \
R=reference_sequence.fasta

And in my tests it complains :

`picard LiftoverVcf -I Test.vcf

ERROR: Invalid argument '-I'.`

Happy to test more on my side

[vineetbansal]

Thanks - also can you run hatchet in this activated conda environment and confirm the version number you're seeing?

[oriolpich]

Hi Vineet, I see

HATCHet v1.0.1