Scripts in R-markdown to transform vcf data for single SNPs into data for visualization and filtering prior to analysis. (based on harbor porpoise analysis in Morin et al. 2019: Data from the dead: genomic SNPs from poor-quality samples detect population structure in North Pacific harbor porpoise (manuscript in prep).
Files for test/demonstration:
- vcf_target_SNP_filter_transform.Rmd
- Ppho_340loc_trimmed2_largefiles_SNP151_minDP10_noIndel_lowGeno.test.vcf.gz
- genotype_changes_100518test.csv
- loci_to_remove_090518.csv
- Loci_recall_minDP15_090518.csv