Question of the format of VCF file for BayesTyper. about bayestyper

[jonassibbesen]

Hi,

BayesTyper support any type of variation as long as it is sequence resolved (ALT column in vcf is nucleotide sequences). bayesTyperTools convertAllele converts allele ids (e.g. <DEL>) to sequences so they can be parsed by BayesTyper. However, the tool only supports the most common types:

* <CNV>
* <CN0>, <CN1>, ...
* <DUP>
* <DEL>
* <INV>
* <INS> (with sequence stored as SEQ in INFO field) 

Other allele ids can be parsed, but the sequence need to be provided as input in a fasta file (see --alt-file).

Best,

Jonas

[zhiyongli1995]

Hi Jonas,

Thanks for your patiently reply, I got your point!
Now I am going to close this issue now.

Best regards,
Zhiyong