Bedaquiline resistance sequence

[pratibha-kadam]

Hello There,

I want to get the bedaquiline resistance gene sequences. Unfortunately the sequences are not present in any of the AMR database. I found mutations but I am not really sure how to incorporate that into a sequence.

In your mutation DB some mutations are gene level and some are on protein level. I am unable to make the sequence.

Can you please guide me on this. I would be really helpful.

[jodyphelan]

Hi @pratibha-kadam

Sadly the pipeline doesn't produce gene sequences. However it does produce a VCF file. You can use bcftools with this and the reference genome to produce a gene sequence. https://samtools.github.io/bcftools/howtos/consensus-sequence.html