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jodyphelan / TBProfiler

Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data
GNU General Public License v3.0
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Bedaquiline resistance sequence #299

Open pratibha-kadam opened 1 year ago

pratibha-kadam commented 1 year ago

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 commented 1 year ago

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