Question: Mpileup is not working
1
gravatar for ridatariq04
3.0 years ago by
ridatariq0430
Pakistan
ridatariq0430 wrote:

Hi

I use Galaxy online on daily basis for analysis of my data. I got problem with Mpileup tool, when I run "MPileup call variants" it display an error and GATK tool also not working. So kindly help me to figure out  these problems.

Thanks

Rida

galaxy • 991 views
ADD COMMENTlink modified 3.0 years ago by Jennifer Hillman Jackson25k • written 3.0 years ago by ridatariq0430

Hi Rida 

I also had general  problems with GATK and more recently Mpileup stopped working for me  so I switched to Freebayes, which I am very happy with.  I would never go back to GATK but it would be nice to be able to do comparisons with Mpileup.

Thanks  Guy

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by Guy Reeves1.0k

Thanks Guy Reeves

ADD REPLYlink written 3.0 years ago by ridatariq0430
0
gravatar for Jennifer Hillman Jackson
3.0 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The MPileup tools is undergoing corrections. Please follow this Github ticket for progress on the resolution: https://github.com/galaxyproject/tools-devteam/issues/255

If you could describe the GATK error in more detail, we may be able to help interpret it (in particular the end of the error message usually has the details of the problem). Or, if working at http://usegalaxy.org, failed datasets (job errors) can be submitted as a bug report for feedback.

Thank you for reporting the problem, Jen, Galaxy team

ADD COMMENTlink written 3.0 years ago by Jennifer Hillman Jackson25k
I am unable to run "Unified Genotyper SNP and indel caller" tool. I always got the error message
"##### ERROR MESSAGE: SAM/BAM file /galaxy-repl/main/scratch/tmp-gatk-EFe8zG/gatk_input_0.bam is malformed: SAM file doesn't have any read groups defined in the header.  The GATK no longer supports SAM files without read groups". Please help to solve this problem.
ADD REPLYlink written 3.0 years ago by ridatariq0430
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