官方github链接：https://github.com/ferdinand-popp/telomerehunter2
参考代码：
telomerehunter2 -ibt TUMOR_FILE -ibc CONTROL_FILE -o OUTPUT_DIRECTORY -p ID_OF_SAMPLE -b BANDING_FILE [options]批量运行脚本：
perl -ne 'chomp; next if /^$/; @a = split /\t/; print "telomerehunter2 -p $a[0] -ibc ../align/$a[1]_bqsr.bam -ibt ../align/$a[0]_bqsr.bam -o /group_homes/prolinying/home/share/Phyllodes/LCM-WGS/telomerehunter2 -b /home/zhoukaiwen/database/telomerehunter2/hg38_cytoBand.txt > log/$a[0].log 2>&1 && echo $a[0] telomerehunter2 ok\n";' ../mutect2/sample_pair.txt > RunTelomereHunter.sh
nohup bash -c "cat RunTelomereHunter.sh | parallel -j 4" > log/telomerehunter.log 2>&1 &结果文件解读：
输出文件为“Tumor_summary.tsv”的即为结果，其中tel_content为端粒长度
PID sample tel_content total_reads read_lengths repeat_threshold_set repeat_threshold_used intratelomeric_reads junctionspanning_reads subtelomeric_reads intrachromosomal_reads tel_read_countgc_bins_for_correction total_reads_with_tel_gc TCAGGG_arbitrary_context_norm_by_intratel_reads TGAGGG_arbitrary_context_norm_by_intratel_reads TTGGGG_arbitrary_context_norm_by_intratel_reads TTCGGG_arbitrary_context_norm_by_intratel_reads TTTGGG_arbitrary_context_norm_by_intratel_reads ATAGGG_arbitrary_context_norm_by_intratel_reads CATGGG_arbitrary_context_norm_by_intratel_reads CTAGGG_arbitrary_context_norm_by_intratel_reads GTAGGG_arbitrary_context_norm_by_intratel_reads TAAGGG_arbitrary_context_norm_by_intratel_reads TCAGGG_singletons_norm_by_all_reads TGAGGG_singletons_norm_by_all_reads TTGGGG_singletons_norm_by_all_reads TTCGGG_singletons_norm_by_all_reads TTTGGG_singletons_norm_by_all_reads ATAGGG_singletons_norm_by_all_reads CATGGG_singletons_norm_by_all_reads CTAGGG_singletons_norm_by_all_reads GTAGGG_singletons_norm_by_all_reads TAAGGG_singletons_norm_by_all_reads
FETB06-BLPT-M tumor 2704.045416 2376228562 90 6 per 100 bp 5 1116591 13770 144649 53817 1328827 48-52 412933523 0.0943326607504448 0.1466427725102566 0.083708358745503 0.0422858504143415 0.0132438824959183 0.0180191314456233 0.0006931812991507 0.0899380346071211 0.0407203712012724 0.0246464461920255 4.965852270569585e-07 7.01111007014316e-07 4.717559657041106e-07 2.2725086661928608e-08 7.221527539235092e-07 3.577096974562837e-07 0 5.260436727298289e-07 1.658089656444421e-07 1.392963645388587e-07
FETB06-BLPT-M control 1775.935218 2160559050 90 6 per 100 bp 5 491170 6264 47324 23042 567800 48-52 276569773 0.0725003562921188 0.1134841297310503 0.0863672455565282 0.0403058004356943 0.0168577071075187 0.0165054868986298 0.0011767819695828 0.0497526314717918 0.0713927967913349 0.0369810859783781 3.3833835738023454e-07 2.615063911352018e-07 3.813827722042589e-07 3.7027453612063976e-08 4.670087586821568e-07 8.192324111669153e-08 0 5.688342561153328e-07 1.383901078750891e-07 2.2077619216193147e-07
FETB06-BLPT-M log2(tumor/control) 0.6065404262406129 0.37976927592854426 0.3698154107408493 -0.0451125885059767140.06918752014628017 -0.34808220635008424 0.12658377480988212 -0.7635424085069049 0.8541585240923169 -0.8100278073435476 -0.5854079539855125 0.5535745987608439 1.422796678527075 0.306801086086286 -0.7043095422598166 0.6288544288572661 2.126444531406144 -0.11282577035913463 0.2607811957223489 -0.6644269987342165