Question: How to extract SNPs from galaxy workflow
gravatar for sureshbabu.angara
15 months ago by
sureshbabu.angara0 wrote:

I exactly followed the below galaxy workflow that contain targetted re-sequencing data for a father mother and child trio.

I was successful in creating all the steps till the end in my galaxy. However, from the variant call format file or galaxy workflow

How many SNPs are there in all three individuals? How to count How do I extract SNPs – single nucleotide variants, insertion/deletion variants, multi-nucleotide variants from the VCF file in all three individuals? How to download variant call format file from galaxy workflow?

I am very new to this field. Please be kind and let me know how to look in the steps of the workflow. I appreciate your time and thank you very much in advance.

alignment snp galaxy samtools • 490 views
ADD COMMENTlink modified 15 months ago by Jennifer Hillman Jackson25k • written 15 months ago by sureshbabu.angara0
gravatar for Jennifer Hillman Jackson
15 months ago by
United States
Jennifer Hillman Jackson25k wrote:


  • To sum the counts from a tabular file, use the tool Datamash.

  • To filter a VCF dataset, use the tool VCFfilter.

  • To download data, please see:

  • To examine the steps of a shared workflow do one of these:

    • Expand the step/tool of interest to review a summary of the settings/parameters.
    • Import the workflow into your account and open it in the workflow editor to review the full details. Clicking on a tool will bring up the settings/parameters/post-job-actions in the far right panel.


Hope this helps! Jen, Galaxy team

ADD COMMENTlink written 15 months ago by Jennifer Hillman Jackson25k
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