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Question: pileup to vcf
2
gravatar for charles.wray
3.8 years ago by
charles.wray • 20
charles.wray • 20 wrote:

Is there a tool on public galaxy that will take pileup file or filter pileup output to VCF?
pileup vcf mpileup galaxy • 1.6k views
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modified 6 months ago by Jennifer Hillman Jackson ♦ 25k • written 3.8 years ago by charles.wray • 20
0
gravatar for charles.wray
3.8 years ago by
charles.wray • 20
charles.wray • 20 wrote:

I figured it out
ADD COMMENT • link written 3.8 years ago by charles.wray • 20
2

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

ADD REPLY • link written 3.8 years ago by Martin Čech ♦♦ 4.9k
0
gravatar for taniamahmood38
6 months ago by
taniamahmood38 • 0
taniamahmood38 • 0 wrote:

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

ADD COMMENT • link written 6 months ago by taniamahmood38 • 0

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 REPLY • link modified 6 months ago • written 6 months ago by Jennifer Hillman Jackson ♦ 25k

Thanks a lot Jen, Galaxy team

ADD REPLY • link written 5 months ago by taniamahmood38 • 0
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