How to make consensus sequence from aligned reads ?

Question

[Info.shi]

We already have sequence reads aligned to a reference genome. How can we extract the final reads that map to a specific gene? To make it clear I want to make a consensus sequence from the reads aligned to each gene. SAMTOOLS suggests the command:

samtools mpileup -uf ref.fa aln.bam | bcftools view -cg - | vcfutils.pl vcf2fq

But it gives many wearied characters after + sign of sequence.

I will thankful if anyone kindly guides me.

[5heikki]

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etc.

I think the "wearied characters" you are talking about are fastq quality score values. Note that vcf2fq outputs fastq, not fasta..