Hi members,
I am trying to use the Scalpel indel caller (http://scalpel.sourceforge.net/) to find indels in WGS files from TCGA. But am...
10 results in 0.0055 seconds.
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Scalpel indel caller running slowly on TCGA WGS BAM files
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samtools mpileup -L argument
Argument -L in samtools mpileup "skips INDEL calling if the average per-sample depth is above INT [250]". Why do we need this option? Why INDELs... -
VarScan somatic indel caller working incorrectly?
Hi
I am seeing a seemingly incorrect somatic indel call using VarScan somatic.
The VarScan output line is
chr2 178883096 T +TAAC... -
CLC BIO for detecting indels in ION Torrent PGM data
Hello everyone,
I was wondering if someone has some experience with using the CLC BIO genomics workbench to call indels in ion torrent... -
Parsing a VCF file for indels
Hello,
I am new to Python and and I am trying to parse a VCF file that has reads containing the flag "INDEL". I want to extract... -
Strelka: Somatic small-variant calling workflow for matched tumor-normal samples
Hello All,
Strelka is a new workflow available to call SNVs and small indels from sequencing data for matched tumor-normal samples. It... -
How to deal with no calls from GATK Unifiedgenotyper for indels
I am working with 454 single-end long-read data for a region on chr6, using hg19 and dbSNP build 135 as references. GATK Unifiedgenotyper with the option... -
Error during GATK SomaticIndelDetector
Hi,
I'm currently working in a pipeline to assess somatic mutations (SNPs/indels) so I am checking the SomaticIndelDetector tool from GenomeAnalysisTK-1.1-25.... -
mpileup consensus behaviour
I am wondering if anyone has any experience calling a consensus genotype from mpileup data. I am curious how the suggested command from samtools docu... -
Dindel crash whilst parsing bam-sorted file
Dear All,
Does have anyone idea what might have cause this crash?
Thanks.
Michal
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dindel --analysis...Last edited by michalkovac; 11-23-2010, 08:28 AM.
