4.4 extractReads

Extract reads overlapping an allele-file

extractReads extracts all reads overlapping an input-allele-file, writing these reads into a new BAM-file.

4.4.1 Input

Required inputs :

--bam Input_bam_file.bam	Input bam file
--alleles alleles.txt	Allele-File

• Filter parameters to apply specific filters for bases and reads.
• Engine parameters that are common to all tasks can be found.

4.4.2 Output

*_extr.bam

BAM file containing extracted reads.

4.4.3 Usage Example