teltale is a program that computes the fraction of telomeric reads in a BAM file. A read is considered telomeric if it contains at least seven consecutive occurrences of the telomere motif TTAGGG or its reverse complement CCCTAA. The fraction of telomeric reads is the number of telomeric reads divided by the total number of reads in the BAM file. Reads marked as Duplicate or Failed QC are ignored and are excluded from the counts. This program is intended for BAM files containing whole-genome sequencing (WGS) data.
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teltale uses the BamTools API, version 2.4.0 or later. Modify the paths below to refer to the BamTools include and lib directories.

$ g++ -std=c++0x -O3 -o teltale -I ~/bamtools/include/ -L ~/bamtools/lib/ teltale.cpp -lbamtools -lz

$ teltale --help

teltale 2.0

Usage: teltale bam_file

The input is a single BAM file. Its name is specifed as the sole command-line argument.

The output is a single line written to the standard output stream containing four tab-delimited values:

• total number of reads in the BAM file
• number of telomeric reads in the BAM file
• fraction of telomeric reads
• name of the BAM file

An error message is written to the standard error stream if the input file cannot be opened or if it is not a valid BAM file.

The time taken by the program is proportional to the size of the input file.

When comparing the fraction of telomeric reads from several BAM files, be sure that the BAM files have the same read length. The fraction computed for a BAM file having a read length of 150 is not directly comparable to the fraction computed for a BAM file having a read length of 100, because it is easier to find a sequence of seven consecutive occurrences in longer reads.

Contact Stephen V. Rice with questions, suggestions, and other feedback.