TT-Mars

TT-Mars: Structural Variants Assessment Based on Haplotype-resolved Assemblies.

Usage

0. Clone TT-Mars from github and cd TT-Mars. Python >= 3.8 is preferred.
1. Create environment and activate: conda create -n ttmars and conda activate ttmars.
2. Run dowaload_files.sh to download required files to ./ttmars_files.
3. Run download_asm.sh to download assembly files of 10 samples from HGSVC.
4. Install packages: conda install -c bioconda pysam, conda install -c anaconda numpy, conda install -c bioconda mappy, conda install -c conda-forge biopython, conda install -c bioconda pybedtools.
5. Run TT-Mars with following steps: run_ttmars.sh includes more instructions. Users can run it to run TT-Mars after setting up.

The main program: run python ttmars.py -h for help.

python ttmars.py output_dir files_dir centro_file vcf_file reference asm_h1 asm_h2 tr_file num_X_chr

Positional arguments

1. output_dir: Output directory.
2. files_dir: Input files directory. ./ttmars_files/sample_name. The directory where you store required files after running dowaload_files.sh.
3. centro_file: provided centromere file.
4. vcf_file: callset file callset.vcf(.gz).
5. reference: referemce file reference_genome.fasta.
6. asm_h1: assembly files assembly1.fa, which were downloaded after running download_asm.sh.
7. asm_h2: assembly files assembly2.fa, which were downloaded after running download_asm.sh.
8. tr_file: provided tandem repeats file.
9. num_X_chr: if male sample: 1; if female sample: 2.

Optional arguments

-n/--not_hg38: if reference is NOT hg38/chm13 (hg19).
-p/--passonly: if consider PASS calls only.
-s/--seq_resolved: if consider sequence resolved calls.
-w/--wrong_len: if count wrong length calls as True.
-g/--gt_vali: conduct genotype validation.
-i/--gt_info: index with GT info. (For phased callsets)
-d/--phased: take phased information. (For phased callsets)
-v/--vcf_out: output results as vcf files (tp (true positive), fp (false positive) and na).
-f/--false_neg: output recall, must be used together with -t/--truth_file.
-t/--truth_file: input truth vcf file, must be used together with -f/--false_neg.

Example Output

Accompanying Resources

Liftover files

Genome coverage files