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Welcome to the SNPs_pipeline wiki!

Phylogeny Construction with SNPs

Pipeline

We received a vcf file where SNPsaurus converted genomic DNA into nextRAD genotyping-by-sequencing libraries (SNPsaurus, LLC). The nextRAD libraries were sequenced on a HiSeq 4000 on two lanes of 150bp reads.

With this pipeline you would be able to:

Modified from http://grunwaldlab.github.io/Population_Genetics_in_R/qc.html

  • Using RStudio 3.4.4 and packages:

genepop, parallel, poppr, dartR, devtools, phytools, seqinr, phylotools, adegenet, pegas, hierfstat

  1. Remove indels (insertions-deletions)

  2. SNPs upper and lower 20% of depth distribution

  3. Delete:

    3.1 Samples (missingness >70%)

    3.2 SNPs (>90%) with a high degree of missingness information

  4. Rewrite vcf file

  • Using RStudio or VCFTOOLS 0.1.17

    1. Run Minor Allele Frequency (MAF)

  • Convert vcf file to PHYLIP format

Suitable for RAxML

Or you can use another tool from CIPRESS Phylogenetic Collection (BEAST2, MRBAYES, RAXML) CyVerse

References

  • http://grunwaldlab.github.io/Population_Genetics_in_R/qc.html

  • RStudio: A Platform‐Independent IDE for R and Sweave - Racine - 2012 - Journal of Applied Econometrics - Wiley Online Library. https://onlinelibrary.wiley.com/doi/abs/10.1002/jae.1278.

  • variant call format and VCFtools | Bioinformatics | Oxford Academic. https://academic.oup.com/bioinformatics/article/27/15/2156/402296.

  • Lischer, H. E. L. & Excoffier, L. PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs. Bioinformatics 28, 298–299 (2012).

  • Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).

  • Miller, M. A., Pfeiffer, W. & Schwartz, T. The CIPRES Science Gateway: Enabling High-impact Science for Phylogenetics Researchers with Limited Resources. in Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the Campus and Beyond 39:1–39:8 (ACM, 2012). doi:10.1145/2335755.2335836.

  • Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 47, W256–W259 (2019).

  • https://www.onworks.net/programs/vcftools-online?amp=0