Tag: Pindel
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…
