Question: Generate Pileup Not Working?
0
Lilach F • 190 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="" d03816="" 1e3fe9072e="" stdout="">
Tool
Standard Error:stderr<https: main.g2.bx.psu.edu="" datasets="" d038161e3fe9="" 072e="" 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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modified 6.5 years ago
by
Jennifer Hillman Jackson ♦ 25k
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written
6.5 years ago by
Lilach F • 190
