37 results in 0.0023 seconds.
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How to get variant allele frequency for internal tandem duplications from Pindel?
I'm using the latest version of Pindel (0.2.5b9, 20160729) for somatic DNA to detect internal tandem duplications (ITDs) at variant allele frequencies... -
optimize a execution of a pindel process
I am looking to optimize a pindel process. Below is the command used:
...Code:pindel -f refererence -i configfile -c ALL -T 16 -o sample
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Issues installing Pindel from git
I'm having issues with installing Pindel from git, even when using the dedicated htslib from git instead of the one packaged from samtools.
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Pindel and GATK AD Concordance
I was hoping to get some advice on working with the AD field for variants in VCFs produced by Pindel and Pindel2VCF.
My lab has a variant... -
Pindel configuration file errors
Hi there,
I'm using Pindel, my configuration file looks like this:
But when I run Pindel I get the following... -
Pindel "per sample" columns
Hello,
I am having trouble interpreting the Pindel "per sample" columns of the output files.
In a previous post it has... -
Pindel considers reads or fragments?
I'm trying to decide how to best set my filters for Pindel. While my insert size is ~150 in a number of samples, we're sequencing 2x100bp, which means... -
Pindel optimisation for exome data
Dear All,
I am trying to optimise Pindel to run on a small set of 12 whole exome samples to detect structural variants. With the latest... -
Problem with Pindel output
Hi,
I have been using normal/tumor GATK processed realigned and recalibrate bam files for mutation , indel and CNV analysis. I have used... -
Pindel memory usage 30x whole genome
How much memory should Pindel be using on a 30x whole genome? With the smallest window size it is using a large amount of memory even when the log says... -
Creating psuedo paired-end sequencing reads from single-end reads
Does anyone know of a program out there that will generate psuedo paired-end sequencing reads from Illumina 100bp single-end reads? This is for an initial... -
Problem for pindel2vcf to create vcf from from pindel-created _D files
I am New pindel user, and use ../pindel -f hg19.fasta -i p1_config.txt -c ALL -o P2_Index_95_P319 to create P2_Index_95_P319 with _SI, _D, and so on.... -
Pindel Algorithm Explanation
Hey,
I am looking at the Kai Ye paper on Pindel:
http://bioinformatics.oxfordjournals...865.full.pdf+h... -
How to run pindel with multithreading?
I was trying to run pindel with multithreading turned on by the following command:
pindel -f Homo_sapiens_assembly19.fasta -i ConfigHF.txt... -
Pindel: Reference counting (Short Insertion)
I have a problem with counting sequences in reference to the Pindel software.
I am analyzing exome data (tumor vs. normal) and found a...
