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:
BWA
select only lines with the pattern Matching pattern: XT:A:U
SAM-to-BAM
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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