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joint SNP calling for individuals with very different coverage
We have sequenced the genome of 40 individuals from two species to do population genomic analyses. For the first species, one of them was sequenced to build a reference genome, at around 90X, ten others are sequenced at around 30X, and nine at 5X. For the second species, one is sequenced at 40X and the rest at 5X. Our idea was to perform a joint SNP calling (per species) without considering the downsampling of the highest sequenced individuals. Otherwise, some people suggest this can be biasing and that all samples should be downsampled to 5X to do a fair SNP calling. Intuitivelly, using the samples at high coverage is very advantageous to detect variants, and from our point of view, this will not introduce biases to the calling of the rest of samples.
Could you please give us your advise and why?
Thanks a lot in advance,