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Make it easier to run downstream GATK calling on downsampled bams #14

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eriqande opened this issue Oct 23, 2024 · 0 comments
Open

Make it easier to run downstream GATK calling on downsampled bams #14

eriqande opened this issue Oct 23, 2024 · 0 comments

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@eriqande
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I just need to add some code and stuff so that this can be specified in the config.

One thought I have is to change the bqsr-round-X directory level into a downsample-X directory level, since I don't think we will ever realistically use the bqsr stuff on non-model organisms.
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@eriqande