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Joint-calling

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This documentation page is incomplete, and we are actively working on improving it with comprehensive information.

Batching​

For larger cohorts, samples should be split up into batches of about 100-500 samples with similar characteristics. We recommend batching based on overall coverage and dosage score (WGD), which can be generated in EvidenceQC. An example batching process is outlined below:

  1. Divide the cohort into PCR+ and PCR- samples
  2. Partition the samples by median coverage from EvidenceQC, grouping samples with similar median coverage together. The end goal is to divide the cohort into roughly equal-sized batches of about 100-500 samples; if your partitions based on coverage are larger or uneven, you can partition the cohort further in the next step to obtain the final batches.
  3. Optionally, divide the samples further by dosage score (WGD) from EvidenceQC, grouping samples with similar WGD score together, to obtain roughly equal-sized batches of about 100-500 samples
  4. Maintain a roughly equal sex balance within each batch, based on sex assignments from EvidenceQC