Data from: Dispersal in the sub-Antarctic: king penguins show remarkably little population genetic differentiation across their range

Clucas GV, Younger JL, Kao D, Rogers AD, Handley J, Miller GD, Jouventin P, Nolan P, Gharbi K, Miller KJ, Hart T

Date Published: October 3, 2016

DOI: http://dx.doi.org/10.5061/dryad.7c0q8

 

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Title King penguin filtered SNP dataset
Downloaded 31 times
Download king_final_snp_dataset.vcf (7.517 Mb)
Download README.txt (4.242 Kb)
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Title BayeScan_output_king_penguins
Downloaded 9 times
Description The output from BayeScan saved as an Excel doc. BayeScan was run on the final dataset of 5154 king penguin SNPs with the prior odds of neutrality set to 5. The columns are in the same order as the standard "yourprefix_fst.txt" output file from BayeScan, but an additional column has been added which maps the input file locus index to the locus index used in the VCF.
Download BayeScan_output.xlsx (394.2 Kb)
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Title Python script for filtering .SAM formatted mapping files aligned with BWA mem
Downloaded 13 times
Description The filter.py script works on sorted .SAM formatted mapping files from BWA mem alignment. For every pair of mapped forward and reverse reads, it parses out the CIGAR field (column 6 of the SAM file) and the MD tag to calculate the number of insertions, deletions, and mismatches. If a pair of reads have mismatches less than or equal to five and insertion/deletions less than or equal to two, then the pair is kept and printed to linux standard output. SAM header lines are ignored by the parser but also printed to standard output for compatible down-stream analysis.
Download filter.py (1.49 Kb)
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When using this data, please cite the original publication:

Clucas GV, Younger JL, Kao D, Rogers AD, Handley J, Miller GD, Jouventin P, Nolan P, Gharbi K, Miller KJ, Hart T (2016) Dispersal in the sub-Antarctic: king penguins show remarkably little population genetic differentiation across their range. BMC Evolutionary Biology 16(1): null. http://dx.doi.org/10.1186/s12862-016-0784-z

Additionally, please cite the Dryad data package:

Clucas GV, Younger JL, Kao D, Rogers AD, Handley J, Miller GD, Jouventin P, Nolan P, Gharbi K, Miller KJ, Hart T (2016) Data from: Dispersal in the sub-Antarctic: king penguins show remarkably little population genetic differentiation across their range. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.7c0q8
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