How to generate consensus sequence for all refs

[sampie]

Hi,

I have been trying to use samtools to create consensus sequences. However, it seems that conseqs.fastq (see command below) is missing consensus sequences for most reference sequences.

--- samtools command ---
samtools mpileup -uf ref.fa sorted.bam | bcftools view -cg - | /usr/share/samtools/vcfutils.pl vcf2fq > conseqs.fastq
----

In IGV, I can create consensus sequence for all references (one by one). I would like to create the consensus sequences with a command line tool like samtools. Is there a way to make samtools to produce all consensus sequences like IGV does?

Thanks

[Antony03]

You should take a look at UGENE. I know this tool can produces consensus with a graphical interface and in command line.

http://ugene.unipro.ru

[sampie]

Thanks for reply! UGENE looks like a good tool. However, I was unable to find out how to build consensus sequence with UGENE command line. Can I have an example of a command that can be used to build consensus sequences from ref.fasta and sorted.bam files?

[sampie]

Hi,

I tried to isolate a ref sequence and try with that. So, I have ref.fasta with only one sequence. I have also sorted.bam which is an alignment against the ref.fasta. It seems samtools is not working even in case of just one reference.

Samtools gives an empty mpileup (that is no lines after "#CHROM POS ID..." line) with command: samtools mpileup -uf ref.fasta sorted.bam | bcftools view -cg -

However, IGV is able to give a consensus sequence (see below). The consensus sequence has only a small sequence (ACGT) portions. Could there be somekind of filtering attached to samtools mpileup, which prevents it from giving the wanted consensus sequence?

Thanks

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NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCACCAGGGC
GACGATGCGTAGCCGGCCTGAGAGGGTGGACGGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTA
GGGAATTTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
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NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCAATAAGTATCCCGCCTGGGGAGTACGG
CCGCAAGGYTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGYATGTGGTTTAATTCGAMGCAACGCGAAGAA
CCTTACCAGGTCTTGACATCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
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