SNPhylo

Quick StartTo use SNPhylo, import your data in VCF, HapMap, Simple SNP or GDS format

• Resources: https://github.com/thlee/SNPhylo

Test Data

Input File(s)

Use Washingtonia_SNPhylo_dataset.recode.vcf from the directory above as test input.

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

• Use these parameters within the DE app interface:
• Maximum_PLCS: 95
• LD_threshold: 1
• MAF_threshold: 0.05
• Missing_rate: 0.8

Output File(s)

Expect these files as output:

• snphylo.output.fasta
  
• snphylo.output.filtered.vcf
  
• snphylo.output.gds
  
• snphylo.output.id.txt
  
• snphylo.output.ml.png
  
• snphylo.output.ml.tree
  
• snphylo.output.ml.txt
  
• snphylo.output.phylip.txt
  
  

Tool Source for App

• https://github.com/thlee/SNPhylo