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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