[feature request] Genotyping more than 500 samples about bayestyper

[jonassibbesen]

Hi, due to how the genotyping algorithm is designed it will unfortunately not scale well too that many samples. What you could do instead is to combine all predicted variants across all 500 samples and then run BayesTyper on each sample independently or in batches using this combined variants set. See here for more information: https://github.com/bioinformatics-centre/BayesTyper/wiki/Executing-BayesTyper-on-sample-batches

Please let me know if you have any other questions.

[Sherry520]

@jonassibbesen I followed the method “Executing BayesTyper on sample batches” to genotyping my samples, when I Combine the the batch vcf files using bcftools merge, Error occured:
Failed to open bayestyper_rmdup_DH_00_unit_1/bayestyper-sk-b73.vcf.gz: not compressed with bgzip
it seems like bayestypre use gzip to commpress the vcf files, But bcftools require bgzip commpressed vcf files

[jonassibbesen]

Thank you for mentioning this. I have updated the wiki with an additional bgzip compression step.