Executing BayesTyper on sample batches

It is currently only possible to run BayesTyper on 30 samples at the time. Hence, to run on more samples:

1. Generate a set of variant candidates across all samples

2. Run BayesTyper on batches of 30 samples or less using variant candidates from all samples as variant input

3. Compress output vcf file from each batch using bgzip (BayesTyper can only output gzip compressed files which is not supported by bcftools)

4. Combine the the batch vcf files using bcftools merge --filter-logic x --info-rules ACP:max -O z -o <output_prefix>.vcf.gz <bayestyper_batch_1.vcf.gz> <bayestyper_batch_2.vcf.gz> ...

   • Important: Please note that non PASS filters are not guaranteed to be consistent after merging