User: Jack

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Jack60
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Posts by Jack

<prev • 9 results • page 1 of 1 • next >
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Pindel Bad_Alloc Error With Window Size 1
... I'm trying to run Pindel on some whole exome tumor/normal pairs. BAMs are about ~40Gb in size. I've got a bad_alloc error at my first trial. Below is the command line. I set the window size to 1; also disabled search for breakpoints and long insertions as suggested in the FAQ: pindel -f ucsc.hg19.f ...
error pindel written 3.5 years ago by Jack60 • updated 3.0 years ago by jenn.drummond20
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Comment: C: Software To Call Somatic Indels?
... I work with exome sequencing data and I do use VarScan for CNV analysis. It works pretty well. As you commented, this is a good stragey for larger indels, perhaps a kilobase or larger... Smaller/weaker calls could get smoothed out by DNAcopy. I need a caller that works between the ranges of a poin ...
written 3.5 years ago by Jack60
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Answer: A: Can Breakdancer Be Used On Bwa Mem Alignments?
... I don't see any reason why you can't. All you need is a BAM file. ...
written 3.5 years ago by Jack60
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Software To Call Somatic Indels?
... I'm looking for a tool to call somatic indels (10-1000bp range, not point mutations) in tumor/normal samples. It looks like GATK doesn't support SomaticIndelDetector or Indelocator anymore. What tools are you using to call somatic indels? Are they well supported? Thanks. ...
somatic cancer written 3.5 years ago by Jack60 • updated 3.4 years ago by Malachi Griffith15k
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Breakdancer Max Kahan Error:0
... I'm using breakdancer-max 1.4.4-unstable-7-6213d5a on exome sequencing data from tumor-normal pairs (all from Illumina HiSeq 2500, 200x coverage, whole exome using NimbleGen Exome v3.0). BAM files are ~40Gb in size, all quality-trimmed using fastqc, aligned using BWA-sampe, processed using GATK pipe ...
breakdancer error written 3.5 years ago by Jack60 • updated 3.4 years ago by ernfrid380
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Comment: C: Somaticsniper Hangs Up
... I've not tested running SomaticSniper only on the unlocalized contigs. Bam files are ~40Gb each. Let me know what you think. ...
written 3.6 years ago by Jack60
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Comment: C: Somaticsniper Hangs Up
... I'm using 1.0.3. It doesn't seem like depth is the problem. Please see the update to my post. I'm happy to share the data, if you'd like to figure out what's going on. ...
written 3.6 years ago by Jack60
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Comment: C: Somaticsniper Hangs Up
... Chris, I've updated the question with more details. Please let me know if you need any other information. Thanks for your help. ...
written 3.6 years ago by Jack60
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Somaticsniper Hangs Up
... I'm running SomaticSniper on whole-exome tumor/normal pairs. A typical run takes a couple hours. One sample, however, keeps running after 24hrs. No error message. I can't figure out why. It doesn't seem to be a hardware problem because other bams from the same dataset process just fine. (all from ...
written 3.6 years ago by Jack60

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