Closed shalabhsuman closed 11 years ago
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?
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.
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:
Hope this helps to get started with.
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
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
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 usingbcbio.variation "0.0.8"
(what particular command to be used to correctly pull the package and dependencies)??Thanks
Shalabh Suman