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.gard...@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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