How to get consensus sequence from .sam file?

[slny]

I'm trying to get consensus sequence from sam file according to the instruction from samtools website as below.

samtools pileup -cf ref.fa aln.bam | samtools.pl pileup2fq -D100 > cns.fastq

However, there is actually no samtools.pl. Is there any way I could get the consensus sequence from sam file?

Thanks

[swbarnes2]

In the latest release, its in the misc folder. And I think the latest release has a vcf2fq subroutine in vcfutils, but it's slow because you have to make a massive all-points .bcf file, and neither program will correct for indels.

[slny]

Yes, I found samtools.pl in misc folder. Thanks.

[dagarfield]

I think you may find this link helpful

http://samtools.sourceforge.net/mpileup.shtml

Pileup is now depreciated.