As an alternative, you can easily install Galaxy on your own computer to negate the upload time.. it's very easy if you have a *nix system: https://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy -K On Thu, Jul 7, 2011 at 11:12 PM, Alison Gardner <alison.gardner@adelaide.edu.au> wrote:

Hello,

I am having trouble replicating the great output you get after running samtools "Filter pileup on coverage & snps with ten columns (with consensus)" when I try to run samtools locally on my computer.

Unfortunately we are unable to use Galaxy with our new data as our files are too large to upload to the website.

Do you use some other scripts in the back ground to get such an informative output?

When I run the samtools commands

samtools pileup -i -vcf RefSeq.fa aln_sorted.bam > aln_ivcf.pileup

and then

samtools.pl varFilter aln_ivcf.pileup | awk '($3=="*" && $6>=20 && $7>=20 && $8>=10)' > final_aln_ivcf.pileup

I do not get useful information in the output that tells me how many reads are calling the alternative allele, & what the alternative allele is.

Any help would be gratefully received.

Thank you

Alison Gardner

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