From reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species

Table 1 Summary statistics for the resultant SNP loci datasets of three pipelines, filtered at a 70% call rate (see Additional file 1: Table S1 for data filtered on 30% call rate), for Tasmanian devil (N = 131) and pink-footed goose (N = 40), including total number of loci (total loci), average number of loci sequenced across individuals (mean loci), amount of missing data (%), calculated error rates (%), mean observed heterozygosity across loci (H_O), mean expected heterozygosity across loci (H_E), and average multilocus heterozygosity of individuals (MLH)

Dataset	Pipeline	CPU hours^a	Total loci	Mean loci (min; max)	% missing	Error rate (%)^b	H_O (± SD)	H_E (± SD)	MLH (± SD)
Devil	Stacks	16	1359	1177.3 (500; 1326)	13.4	2.9	0.207 (0.149)	0.248 (0.163)	0.205 (0.043)
	SAMtools	55	251	205.8 (96; 236)	18.0	6.6	0.308 (0.160)	0.327 (0.115)	0.298 (0.092)
	GATK	325	1464	1297.2 (604; 1442)	11.4	5.3	0.185 (0.139)	0.256 (0.161)	0.184 (0.040)
Goose	Stacks	11	52,053	44,914.4 (954; 50,517)	13.7	NA	0.132 (0.127)	0.156 (0.136)	0.127 (0.026)
	SAMtools	14	26,437	22,035.0 (732; 23,732)	16.7	NA	0.256 (0.160)	0.307 (0.142)	0.563 (0.158)
	GATK	65	277,362	245,412.2 (6787; 270,0084)	11.5	NA	0.137 (0.121)	0.187 (0.149)	0.132 (0.034)

^aCPU hours represent total computational time for each pipeline excluding alignment and the further filtering in R. Note that while some steps can be parallelised for quicker computation, not all steps allow for this
^bError rates could not be calculated for the pink-footed goose dataset as no replicates were included in the current analysis. Error rate is calculated after filtering on SNPs with > 85% reproducibility, so is lower than initial error rates

ISSN: 1471-2164