consensus sequence

[mmmm]

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??

[GenoMax]

See this thread: http://seqanswers.com/forums/showthread.php?t=14565 (and the other thread mentioned in #4 there).

[mmmm]

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?

[swbarnes2]

You don't literally use < > around the file names.

[mmmm]

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???

[GenoMax]

but where should I put the output file name???

$ samtools mpileup -uf reference.fasta sorted_alignment.bam | bcftools view -cg - | vcfutils.pl vcf2fq > output_file_name

[mmmm]

yes- thanks.
I will ignore the abnormal shapes that appeared after the sequence
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