bcbio.variation

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this is my vcf file i don't understand MAXGT and POLY. how to remove MAXGT AND POLY, i am go to gwas study but thia MAXGT AND POLY was my...

karthickji

Hello The "bcbio.variation-0.2.6-standalone.jar" file contains several URL that has log4j. Tenable reports log4 vulnerability on the server. The server has no log4j installed. My problem is how to solve log4j...

kadex-ux

Error with variant-utils comparetwo: Structural variant type not handled: :NON_REF

2

I am trying to use the variant-utils comparetwo function to compare two gvcf files from our GATK pipeline. I have tried several iterations of files including converting to vcf using...

ragans

support for non human data.

2

Hi! Does this software support for non human diploid data like bovine with 29 autosomes? best, Tim

timknut

bcbio.variation-0.2.1 standalone errors

1

I downloaded the most recent standalone version of bcbio.variation (https://github.com/chapmanb/bcbio.variation) in order to generate a summary of concordance between two call sets and encountering some issues, I ran the command...

ssaif

format of input files: java.lang.NumberFormatException: For input string:

7

Hi, I am trying to compare a set of vcf files to a set of confirmed snps from a genome in a bottle database. I do not have access to...

zeneofa

Out of bounds error during normalization: freebayes

7

Hi Brad, I reran the same files with 0.2.1 and received a different set of errors. It again halted during the processing/normalization of the freebayes joint calling file. If I...

stsmall

Error at the validation step

7

Hello, I am trying to incorporate the ensemble approach in my bcbio analysis and getting errors at the bcbio.variation command for validation of calls. Here are some details, Run log...

ssaif