Question: pileup to vcf
2
gravatar for charles.wray
3.4 years ago by
charles.wray20
charles.wray20 wrote:

Is there a tool on public galaxy that will take pileup file or filter pileup output to VCF?

pileup vcf mpileup galaxy • 1.2k views
ADD COMMENTlink modified 23 days ago by Jennifer Hillman Jackson25k • written 3.4 years ago by charles.wray20
0
gravatar for charles.wray
3.4 years ago by
charles.wray20
charles.wray20 wrote:

I figured it out

ADD COMMENTlink written 3.4 years ago by charles.wray20
2

If you feel so inclined posting a link to the tool you used might be helpful to others facing the same situation.

ADD REPLYlink written 3.4 years ago by Martin Čech ♦♦ 4.7k
0
gravatar for taniamahmood38
23 days ago by
taniamahmood380 wrote:

Could you please tell me how you did it (made a vcf file from pilup dataset ) ? I am facing the same problem.

ADD COMMENTlink written 23 days ago by taniamahmood380

Options:

  • Input pileup and output VCF: NGS: Variant Analysis > Varscan
  • Input BAM and output VCF: NGS: SAMtools > MPileup
  • Input BAM and output BCF: MiModD > MiModD Variant Calling

Thanks! Jen, Galaxy team

ADD REPLYlink modified 23 days ago • written 23 days ago by Jennifer Hillman Jackson25k

Thanks a lot Jen, Galaxy team

ADD REPLYlink written 8 days ago by taniamahmood380
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