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



___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to