Question Posted 01/17/18:

I have obtained the bam files for a number of samples for my project. However, I am struggling to find within them the discordant/partially mapped reads. Having looked through the Casava manual, could you confirm that the bam files I have no not contain the unmapped (repeatmasked and non-unique) reads, and they are stored in another directory on your system (suggested by '--sortKeepAllReads' tag)? If so, how can I obtain the data in the 'Nonmapped' directory for the samples?

My project involves using transposable element detection tools (MELT, TEBreak, etc) to identify the coordinates of transposable elements within the ADNI samples. The tools require the discordant/unmapped reads within the bam file in order to do this.

Kindest regards,
Response posted 01/17/18 by Kwangsik Nho:
All BAM files in ADNI WGS data contain all raw reads regardless of mapped or unmapped.