Tag: Pindel
I cannot find the file in configuration file
Pindel Error: I cannot find the file in configuration file 1 Hi, I come across this error while running pindel v0.3 in docker my bam file is named as “main.clean.bam” and my config file has : main.clean.bam 270 main The error is: I cannot find the file ‘main.clean.bam’. referred to…
Study on detection of CNVs using human whole genome bisulfite sequencing data
It has been reported that the aberrant DNA methylation may result in copy number variations (CNVs), and the CNVs may alter the levels of DNA methylation. Whole genome bisulfite sequencing (WGBS) is able to generate the sequencing data of DNAs, and shows the potential ability to detect CNVs. However, the…
long run-time and low CPU usage
Pindel: long run-time and low CPU usage 0 I’m trying to run Pindel on some 30x Illumina WGS data. I aligned reads with BWA-MEM, then sorted by co-ordinates and indexed them with Samtools. I also tried filtering the bam files with samtools -F 0x800 as suggested by another post. I…
Issues installing Pindel from git
Issues installing Pindel from git 1 I’m currently attempting to install Pindel on my ubuntu machine (16.04 server), but have been having issues with running the ./INSTALL file. The ./INSTALL file takes the path to htslib as an argument, so I also installed htslib from git with git clone github.com/samtools/htslib…
the Genomic Rearrangement IDentification Software Suite
Tool:GRIDSS: the Genomic Rearrangement IDentification Software Suite 0 GRIDSS is typically used for detecting structural variation breakpoints from short read sequencing data but is a modular software suite containing a number of tools useful for the detection of genomic rearrangements including: A structural variant caller. The GRIDSS caller uses break-end…
