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 jen@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

---

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/

-- Jennifer Jackson http://galaxyproject.org