Question: Using Galaxy to sort SNPs according to their allele frequency
gravatar for adirsommer
6 months ago by
adirsommer0 wrote:


I have a list of SNPs uploaded to the Galaxy platform ( and I'm looking to sort them according to their allele frequency. Can someone please guide me through the process?

Thank you.

snp galaxy • 200 views
ADD COMMENTlink modified 6 months ago by Jennifer Hillman Jackson25k • written 6 months ago by adirsommer0
gravatar for Jennifer Hillman Jackson
6 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Are the SNPs in VCF format? The tools in the group NGS: VCF Manipulation can be used to summarize (count), filter on alleles, modify the formatting to be in a tabular format (aka "Tab-delimited") and many other operations.

VCF data is more useful in coordinate sorted format, not allele frequency when used with downstream tools, so there is no specific tool for that, however, those counts output in tabular format can be sorted with Filter and Sort > Sort data in ascending or descending order and used any way you want for custom queries/manipulations.

If this does not help, please explain your starting input format/source in more detail.

Galaxy tutorials, including the 101 that includes some basic text manipulation operations:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 6 months ago by Jennifer Hillman Jackson25k
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