Re: [galaxy-user] generate pileup not working?

[Lilach Friedman]

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 
>
> 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
>
>
>
> ___
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>
>
> --
> Jennifer Jackson
> http://galaxyproject.org
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Re: [galaxy-user] generate pileup not working?

[Jennifer Jackson]

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 quality60
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/prep40




___
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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
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--
Jennifer Jackson
http://galaxyproject.org

___
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Galaxy analysis and other features on the public server
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[galaxy-user] generate pileup not working?

[Lilach Friedman]

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
pileupfrom
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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Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
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use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

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please use the interface at:

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