Question: Generate Pileup Not Working?
0
gravatar for Lilach F
6.2 years ago by
Lilach F190
Lilach F190 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
bwa alignment samtools bam • 1.2k views
ADD COMMENTlink modified 6.2 years ago by Jennifer Hillman Jackson25k • written 6.2 years ago by Lilach F190
0
gravatar for Jennifer Hillman Jackson
6.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:
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 // -- Jennifer Jackson http://galaxyproject.org
ADD COMMENTlink written 6.2 years ago by Jennifer Hillman Jackson25k
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> input with this tool) and let us know if you continue to have problems. data 94: converted BAM print the mapping quality as the last column all lines calling model 0.85
ADD REPLYlink written 6.2 years ago by Lilach F190
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