Generate consensus from a BAM file to each of the variants

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3.5 years ago

fhsantanna ▴ 620

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 • 1.0k views

ADD COMMENT • link 3.5 years ago by fhsantanna ▴ 620

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How about using GATK FastaAlternateReferenceMaker (LINK).

ADD REPLY • link 3.5 years ago by GenoMax 148k

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Seems promising, I'll give you a feedback.

ADD REPLY • link 3.5 years ago by fhsantanna ▴ 620

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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?

ADD REPLY • link 3.5 years ago by fhsantanna ▴ 620

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