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
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.


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
Tool Standard 
 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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