Generate consensus sequence with Samtools mpileup?

[Heisman]

Hey all,

I have been unable to do this. When running the two lines of code shown here at the top (http://samtools.sourceforge.net/mpileup.shtml) it states that -u is an illegal option. This is with version 1.18. Has anybody else experienced this or do any of you have a way to generate the consensus sequence?

[Heisman]

Nevermind, we got it to work with this:

./samtools mpileup -uf /<reference_seq.fa> <aligned_file.bam> | /samtools-0.1.18/bcftools/bcftools view -bcg - > <intermediate.bcf>

/samtools-0.1.18/bcftools/bcftools view <intermediate.bcf> > output.txt

[MaskedMicrobiologist]

Consensus Making

This is great! It solved the problem I've been having with a bit of resequencing. Do you know of any way to turn this into fasta format, or is there a better execution of this?

I'm trying to use this to close some mispairings in my genome, using Bowtie, followed by this. It's removed all of my "N's", but now I need to write it out to fasta.

Thanks

[krobison]

See previous thread http://seqanswers.com/forums/showthread.php?t=11536

[ahudel]

I've just gotten the hang of the Tuxedo pipeline, but I'm new to samtools. Right now I have a bunch of genes that were unnamed according to my annotation, but I can view the reads and their consensus for each transcript in samtools tview, after getting the genome coordinates from cummeRbund. Does anyone know of a way I can give samtools a genomic coordinate from cummeRbund and so it will give me a consensus sequence for all the reads that map to that section, even if there are multiple exons? Thanks.