Software for genomic structural variant detection and description.
- Download the latest release:
wget https://github.com/Dr-TSteimle/sv-finder/releases/download/1.1.0/sv-finder
- Make the file executable:
chmod +x sv-finder
You can also install the latest version directly from the GitHub repository using cargo:
cargo install --git https://github.com/Dr-TSteimle/sv-finder./sv-finder -h
Usage: sv-finder [OPTIONS] --bam-path <BAM_PATH> --fasta-ref-path <FASTA_REF_PATH> --cytobands-path <CYTOBANDS_PATH>
Options:
-b, --bam-path <BAM_PATH>
-f, --fasta-ref-path <FASTA_REF_PATH>
-o, --output-prefix <OUTPUT_PREFIX> output file prefix [default: sv-finder]
-p, --threads <THREADS> [default: 1]
-c, --cytobands-path <CYTOBANDS_PATH> a cytoband decompressed file, tsv with columns: contig, start, end, cytoband, content.
- hg19: https://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/cytoBandIdeo.txt.gz
- hg38: https://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/cytoBandIdeo.txt.gz
--distance-threshold <DISTANCE_THRE> maximum distance in nucleotids between two misaligned reads
for trying to assemble them together
[default: 350]
--min-overlapping <MIN_OVERLAPPING> minimum overlapping length (nt) required for assembling
two reads together
[default: 50]
--max-consecutive <MAX_CONSECUTIVE> maximum number of consecutive overlapping mismatch
allowed for assembling reads together
[default: 1]
--max-mismatches <MAX_DIFFS> maximum number of overlapping mismatch allowed for
assembling reads together
[default: 3]
--min-reads <MIN_READS> minimum reads per cluster
[default: 10]
-r, --repeat-masker-path <REPEAT_MASKER>
repeat masker gz file path from UCSC (rmsk.txt.gz)
- hg19: https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/rmsk.txt.gz
- hg38: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/rmsk.txt.gz
-h, --help Print help (see more with '--help')
-V, --version Print version
sv-finder minimal needed parameters are :
- A sorted BAM file with it's corresponding BAI index file in the same directory.
- The reference FASTA file used for alignement.
- A cytoband TSV file with coordinates from the same reference file (your should decompress and then recompress the file with bgzip).
- For hg19 you can download it from: https://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/cytoBandIdeo.txt.gz
- And for hg38: https://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/cytoBandIdeo.txt.gz
Defaults parameters should be adequate for small reads analysis.
The algorithm is multi-threaded and written in rust 🦀 for faster processing.
The output is a TSV file with the following columns:
- Name of the cluster.
- Genomic coordinates relatives to the reference and to the query (contig:reference_start-reference_stop|query_start-query_stop), the ranges are 1-based and inclusive.
- The hgvs unique variant identifier.
- The assembled sequence.
Example of a t(10;14) TLX1-TRD observed in an ALL-T sample with it's derivative:
chr10:821|chr14:80_0 chr14:22907700-22908008|1-309;chr10:102890895-102890934|320-359 chr14:g.22908008_qter[CGTAGCCCCC;chr10:g.102890895_qter] GTTAATACTTTACAGTTTTATTACTAGAGGGTTAAAATCCTTTTTCAAGTCTGATAATCAATGATTAACTTTCTTCATTTGTCCTTCACCCATTTGTTTTTTAGGTTGATGGTGTTTTACTTATTGATTTGTGTAATTATAATAATTTTGTGTCTGAGTTTTACAGCATTTAACCACAAAAACAGCATTGGTGAAAGGAGTTTCAGGGGTATTGTGGATGGCAGCGGGTGGTGATGGCAAAGTGCCAAGGAAAGGGAAAAAGGAAGAAGAGGGTTTTTATACTGATGTGTTTCATTGTGCCTTCCTACCGTAGCCCCCGATCTCTGGCTCCGGCATCTGTCTCGGCTTCTGGCGTTCCTGGCCCGCGCGGCGGGCCGCCCTC
chr10:821|chr14:81_1 chr14:22918338-22918105|1-234;chr10:102890891-102890827|240-304 chr14:g.22918105_qterinv[TACCG;chr10:g.102890891_qterinv] ACCCAAGGAAGAACAGCAGTGAGTGAGAGGTCAGCAGCTGTGGTCATCTCCCTGGTCCAGTCAACTTCCTGCTATCCCTTCCAGGCCCCAAAGCAGGGAGGGAAGCTGCTTGCTGTGTTTGTCTCCTGAGGCATGGGACCCAGGGTGAGGATATCCCAGGGAAATGGCACTTTTGCCCCTGCAGTTTTTGTACAGGTCTCTGTAGGTTTTGTAGCACTGTGCGTATCCCCCAGTACCGTGGGACGGAGACCAAGACTCGGAGTAGTTCATGAAGAGAGAGAAGAGGGGAACAAGGCGAGGCTTA