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Generate consensus from a BAM file to each of the variants

I found a putative SARS-CoV-2 co-infection case. After examining the bam file, I found that some positions present two variants. Is it possible to build two consensus, one to the major (most frequent) and one to the minor form (less frequent) of the viral sample?

bam coinfection consensus ivar
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written by fhsantanna fhsantanna

How about using GATK FastaAlternateReferenceMaker (LINK).

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written by GenoMax GenoMax

Seems promising, I'll give you a feedback.

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written by fhsantanna fhsantanna

Dear GenoMax , let me see if I understood. I managed to generate the alternative reference, now do I have to map the reads of my sample to this reference in order to generate a new consensus?

Since the alternative reference was generated over the mn908947 (wuhan), there is no gaps in the sequence, which are originally found in my sequence of interest.

Or should I map the reads of my sequence of interest to its own consensus, then generate the alternative sequence using FastaAlternateReferenceMaker?

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written by fhsantanna fhsantanna

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