We have ~2000 low coverage (mean = 2.6x) whole-genome sequenced bird samples? How best should we impute repeat samples? Should we:
1) merge aligned reads from repeat samples (improving coverage of the individual sampled)
or
2) impute each of the samples (useful to compare genotypes of repeat sampling, or compare differences between sampling date)
or
3) impute only the best coverage repeat sample
We have ~2000 low coverage (mean = 2.6x) whole-genome sequenced bird samples? How best should we impute repeat samples? Should we: 1) merge aligned reads from repeat samples (improving coverage of the individual sampled) or 2) impute each of the samples (useful to compare genotypes of repeat sampling, or compare differences between sampling date) or 3) impute only the best coverage repeat sample