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 |