filter haploid SNP data for use with STRUCTURE
I have genotype dataset of 100+ bacterial isolates and I would like to assess genetic population structure using the program STRUCTURE (or fastSTRUCTURE).
Is there a way to pull non-neutral SNPS so I am not violating the model assumptions? any help is appreciated!
• 871 views
•
link
written
by
goatsrunfaster •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
What can cause Faststructure to produce really high K clusters as optimal (e.g. 12 - 14)
written by Drew •
-
Genetic Model when running PCA
written by Mengna Zhang •
-
How to filter and impute missing snps in vcf file
written by Kumar
-
how to align sequences in multifasta
written by goatsrunfaster •
-
looking for a way to identify a specific gene, and in varying numbers across multiple genomes.
written by goatsrunfaster •
-
differential expression analysis with z score normalized microarray data
written by gracie •
-
FORMAT 'PL' is not defined in the header, assuming Type=String (bcftools)
written by goatsrunfaster •
-
Highly similar bacterial genomes
written by karthic
-
SNPs detection in transcriptomics to define genetic variation between individuals
written by roncalli •
-
What Is An Appropriate Software For Simulating Haplotype Structure In A Pedigree?
written by Rubal •
