BCOR_ITD_ext is a perl script for detecting, annotating, and quantifying BCOR-ITDs (within exon 15) in paired-end NGS data.
Type "perl BCOR_ITD_ext.pl" for usage and options Input: bamfile or fastq files (R1 and R2)
- This script is intended for DNA NGS, however may be applied to RNA NGS (flag -rna) by extracting reads from a reduced locus within exon 15 to avoid spliced reads
Before running perl script for first time:
- Create a bwa index for the BCOR target locus from the provided fasta file ("bwa index -p BCOR_dna_e15 BCOR_dna_e15.fa") and modify script to provide path of the index if necessary (variable $refindex).
- Download following software tools as needed and add to path (or modify script with paths): bwa, samtools, sumaclust, fgbio, bbduk, bedtools, java, picard.