Hi Jen,
Thank you!
It worked on the original BWA, only when it is aligned to hg19 (failed when
the alignment was to hg_g1k_v37.

However, it doen't work on BAM or SAM files after sorting with Select
Matching pattern: XT:A:U
or after filtering the BWA results with Filter SAM on bitwise flag values.

Is there any solution?

Thanks,
   Lilach





2012/6/18 Jennifer Jackson <j...@bx.psu.edu>
>
> Hello Lilach,
>
> Please try running pileup on the original BWA output - (SAM is an OK
input with this tool) and let us know if you continue to have problems.
>
> Hopefully this helps,
>
> Jen
> Galaxy team
>
>
>
>
> On 6/14/12 1:36 PM, Lilach Friedman wrote:
>
> Hi,
> I am trying to do variants call with "generate pileup".
> My steps where:
> 1. BWA
> 2. select only lines with the pattern Matching pattern: XT:A:U
> 3. SAM-to-BAM
>
> 4. then I tried to use "Generate pileup from BAM dataset"
> However, it does not work, and I get the error message:
>
> 114: Generate pileup on data 97: converted pileup
> 0 bytes
> An error occurred running this job: Samtools Version: 0.1.16 (r963:234)
> Error running Samtools pileup tool
> Floating point exception
>
> Did I do anything wrong, or is it a bug?
> The parameters are copied below.
>
> Thanks,
>    Lilach
>
> The parameters are:
>
> Tool: Generate pileup
> Name: Generate pileup on data 97: converted pileup
> Created: Jun 14, 2012
> Filesize: 0 bytes
> Dbkey: hg_g1k_v37
> Format: tabular
> Tool Version:
> Tool Standard Output: stdout
> Tool Standard Error: stderr
>
> Input Parameter Value
> Conditional (refOrHistory) 0
> Select the BAM file to generate the pileup file for 97: SAM-to-BAM on
data 94: converted BAM
> Whether or not to print the mapping quality as the last column Do not
print the mapping quality as the last column
> Whether or not to print only output pileup lines containing indels Print
all lines
> Where to cap mapping quality 60
> Conditional (c) 1
> Theta parameter (error dependency coefficient) in the MAQ consensus
calling model 0.85
> Number of haplotypes in the sample 2
> Expected fraction of differences between a pair of haplotypes 0.001
> Phred probability of an indel in sequencing/prep 40
>
>
>
> ___________________________________________________________
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> --
> Jennifer Jackson
> http://galaxyproject.org
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