Commands, scripts, and results of the xTea paper

Commands to run different tools

Folder run_tools contains the commands used to run different tools. Each subfolder is for one tool, which contains the results used in the comparisons

Benchmark data

Folder benchmark contains the HG002 benchmarked data (coordinate based on hg38).

NA12878 L1 calls

Folder NA12878_L1_cmp contains the L1 comparison between xTean and another "L1 benchmark" released in the PALMER paper (Zhou, Weichen, et al. NAR 2019).

Genotype

Folder Genotype_cmp contains the comparison with one set of PCR validate genotype "benchmark" (Payer, Lindsay M., et al. PNAS 2017).

CHM13 Centromeric L1

Folder CHM13_centromere_L1 contains the RepeatMasker annotation of CHM13 v1.0 assembly and the selected full length centromeric L1. And also xTea's output of the detected ghost L1s.

Scripts to compare two results

We developped x_cmp.py for results comparison. To run it:

python x_cmp.py -L --list multi_platform_rslts.txt  --bcmk bcmk.vcf  --extnd 100 -o cmp_multi_platform.rslt

Where,

-L: indicates this is comparing a list of results;
--list: is the result list in a file with each line in format `result_path TE-Type ID`;
--bcmk: is the benchmark file;
--extnd: is the slack value when comparing two breakpoints;
-o: is the output prefix