Question: Generate Pileup Not Working?
6.4 years ago by
Lilach F • 190
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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