Elwha, Cowlitz, Lyre, Fraser, Skeena, Nass, Kemano, Grays, Sandy, Klamath
Individuals for Elwha and Lyre were accidentally collapsed into one individual. With this analysis, files have been de-multiplexed, aligned to genome, processed through stacks and output VCF file. VCFvisuals.html is preliminary look at coverage for individuals and sites and a PCA for a roughly filtered VCF (filtered individuals with missingness > 0.5, individuals that are duplicated between old and new, and site missingness <0.5, and variants with MAF <0.05 )
Individuals were analyzed to see if any were duplicates (two were identified - 51985.7 and 51985.8 from Klamath - and only one was retained for further analyses).
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Rerun entire pipeline for elwha-lyre individuals that were not separated in processed radtags
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combine oldNEB and newNEB alignments in analysis
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Remove 51889.9_Elwha which was identified as longfin smelt by Krista (COI results)
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Re-run stacks and populations with these above changes, include variant call quality scores in output
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