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have mapped illumina PE reads to the reference genome using BWA and now, would like to get a consensus sequence of the mapped reads- can samtools be used on the aligned bam file??
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See this thread: http://seqanswers.com/forums/showthread.php?t=14565 (and the other thread mentioned in #4 there). -
samtools mpileup -uf /<reference.fasta> <aligned.bam> | bcftools view -bcg - > <intermediate.bcf>
gave me an error: -bash: syntax error near unexpected token "<
I was wondering BCFtools are part of samtools, right?- is this the correct comand?Comment
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You don't literally use < > around the file names.Comment
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has anyone tried this command to generate a consensus file
samtools mpileup -uf reference.fasta sorted_alignment.bam | bcftools view -cg - | vcfutils.pl vcf2fq
but where should I put the output file name???Comment
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Originally posted by mmmm View PostCode:$ samtools mpileup -uf reference.fasta sorted_alignment.bam | bcftools view -cg - | vcfutils.pl vcf2fq > output_file_name
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yes- thanks.
I will ignore the abnormal shapes that appeared after the sequence
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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