bcbio.variation using Lein

[shalabhsuman]

Hello,

I am uncertain how to correctly install and use bcbio.variation as a library from Leiningen.

I have gone through the documentation, but it didn't help much.

I have installed the lein shell script inside /bin, but not sure how to proceed after that...in other words, how to start using bcbio.variation "0.0.8" (what particular command to be used to correctly pull the package and dependencies)??

Thanks

Shalabh Suman

[chapmanb]

Shalabh; Perhaps it would help to understand your specific goal with bcbio.variation. The leiningen route is meant to use it as a library from other Clojure code. Is that what you're trying to do, or use some particular functionality?

[shalabhsuman]

I am trying to install bcbio.variation, so I can test it as a standalone package on multiple VCF files and generate the ensemble results in a single VCF file. I have already installed the bcbio.variation-0.0.9-standalone.jar, however I was not clear how to start using the jar for ensemble process.

On the secondary note, if its possible, I would also like to learn how to use the bcbio.variation as a library from other Clojure code via the leiningen route.

[chapmanb]

Shalabh; Thanks much for the explanation. I wanted to be sure you had the same goals we'd discussed. I put together an initial interface along the lines of our e-mail conversation. Documentation on usage is here:

https://github.com/chapmanb/bcbio.variation#ensemble-variant-calls

This requires a snapshot release of the code from today available here:

https://s3.amazonaws.com/bcbio.variation/bcbio.variation-0.1.0-SNAPSHOT-standalone.jar

This provides a proof of concept but will eventually need additional work for your use case:

• We need to investigate approaches for combining 2-approach combinations. Previously 3-approach combinations were helpful in resolving variants to trust (2 out 3 callers), but I don't yet have a good way to do this with only 2 callers.
• It would be nice to incorporate more information from multi-sample calls. Currently this extrapolates what was done with single sample to multi-sample, but we have additional information in multi-sample that could be leveraged.
• Multi-sample ensemble combinations need speed improvements.

Hope this helps to get started with.

[shalabhsuman]

Thanks for the response.

Right now we are generating multi-sample VCF files using 2 methods (GATK UnifiedGenotyper & FreeBayes), but since you suggested 3-approach combinations, I would generate a third multi-sample VCF file using GATK HaplotypeCaller, so I can test the ensemble variant calling using bcbio.variation-0.1.0-SNAPSHOT-standalone.jar.

Let me run a ensemble test using these 3 VCF files' combination. I will keep you in the loop.

Thank you

Shalabh Suman

[shalabhsuman]

Hello,

So finally I have been able to arrange 3 multi-sample VCF files (GATK UnifiedGenotyper, FreeBayes, VarScan); and I am trying to test ensemble variant calling using the following command:

java -Xmx32g -jar bcbio.variation-0.1.0-SNAPSHOT-standalone.jar variant-ensemble params.yaml /mnt/nfs/gigantor/ifs/DCEG/CGF/Resources/Data/genome/hg19_canonical_correct_chr_order.fa ./output/out.vcf gatkUG_baa.vcf freebayes_baa.vcf varscan_baa.vcf 

I get the following error (screenshot below):

PS: For params.yaml, I am using the exact same example config file provided on your website (https://github.com/chapmanb/bcbio.variation/blob/master/config/ensemble/combine-callers.yaml). Also, I am using the snapshot version of the jar instead of the standard one.

Please suggest.

Shalabh Suman