Change pileup to vcf format allowing for great depth (100.000 reads)???

mpileup
vcf
variant
varscan
freebayes

#1

Hi again!
I am working with RNA viruses for which I need great depth in each position in order to correctly call variants. At the moment I have my pileup formats derived from mpileup algorithm, however when I try to convert them to vcf files using VarScan the Minimum read depth can be set only up to 200, and I need at least 100.000. Is there a way to do it through the galaxy server or I need to do it only with commands? If so, I would appreciate the command with any explanations necessary to do it as I am not command savvy.
Thanks again

admin-edit Linked topic Mpileup with vcf output? How to change galaxy to older version?


Mpileup with vcf output? How to change galaxy to older version?
#2

Public servers often have limits applied to max read depth due to the computational resources available at that server.

  • Mpileup max read depth = 1024
  • Varscan max read depth = 200
  • Freebayes max read depth = default is to evaluate “all best alleles”

If you should decide to use Freebayes instead, review the pre-sets under the form option: Choose parameter selection level. Each “pre-set parameter” choice is described in the tool form. The “full parameter” choice allows you to tune all settings on your own. If you pick your own settings, be aware that this can create a job that is too large and may fail for resource reasons.

Help for jobs that run out of resources at public Galaxy servers, including how to set up your own Galaxy where you can control the resources. Note: allocating more resources won’t solve all “resource” failures as tools have native limits (whether used in Galaxy or not).