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Question: Mpileup is not working
1
gravatar for ridatariq04
3.1 years ago by
ridatariq04 • 30
Pakistan
ridatariq04 • 30 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 • 1.0k views
ADD COMMENT • link •
modified 3.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.1 years ago by ridatariq04 • 30

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 REPLY • link modified 3.1 years ago • written 3.1 years ago by Guy Reeves • 1.0k

Thanks Guy Reeves

ADD REPLY • link written 3.1 years ago by ridatariq04 • 30
0
gravatar for Jennifer Hillman Jackson
3.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 3.1 years ago by Jennifer Hillman Jackson ♦ 25k 
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 REPLY • link written 3.1 years ago by ridatariq04 • 30
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