Code:
samtools mpileup -uf ref.fa aln.bam | bcftools view -cg - | vcfutils.pl vcf2fq > cns.fq
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see http://samtools.sourceforge.net/mpileup.shtml
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Hi adaptivegenome. Could you help me out with building a consensus FASTA from a single BAM file? Thank you.Leave a comment:
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building a consensus FASTA from BAM(s)
Building a FASTA consensus sequence from a single BAM file is straightforward. However, if I had several BAM files representing a number of genomes in a population, and I wanted to build a single consensus of all of these BAM files, would I simply get the consensus of all the reads in all the BAMs for each position?
Also, how are positions where equal numbers of reads support a different base resolved?
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The COVID-19 pandemic highlighted the need for proactive pathogen surveillance systems. As ongoing threats like avian influenza and newly emerging infections continue to pose risks, researchers are working to improve how quickly and accurately pathogens can be identified and tracked. In a recent SEQanswers webinar, two experts discussed how next-generation sequencing (NGS) and machine learning are shaping efforts to monitor viral variation and trace the origins of infectious...03-24-2025, 11:48 AM -
This year’s Advances in Genome Biology and Technology (AGBT) General Meeting commemorated the 25th anniversary of the event at its original venue on Marco Island, Florida. While this year’s event didn’t include high-profile musical performances, the industry announcements and cutting-edge research still drew the attention of leading scientists.
The Headliner
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