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 <https://main.g2.bx.psu.edu/tool_runner?tool_id=sam_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 <https://main.g2.bx.psu.edu/datasets/d038161e3fe9072e/stdout> Tool Standard Error: stderr <https://main.g2.bx.psu.edu/datasets/d038161e3fe9072e/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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