# Research Object Crate for PISAD - Phsaed Intraspecies Sample Anomalies Detection tool

Original URL: https://workflowhub.eu/workflows/1322/ro_crate?version=1

# PISAD - Phsaed Intraspecies Sample Anomalies Detection tool ## Summary We developed PISAD, a tool designed to detect anomalies in cohort samples without requiring reference information. It is primarily divided into two stages. Stage 1: We select low-error data from the cohort and conduct reference-free SNP calling to construct a variant sketch. Stage 2: By comparing the k-mer counts of other cohort data to the variant sketch, we infer the relationships between the sample and other samples to detect the sample swap. ## Dependencies recommend use conda to install - GCC (Tested on 8.5.0) - gperftools(2.10) - hdf5(1.14.3) - boost(1.85.0) ## Installation cloning the PISAD repository to your machine and enter its directory. ```bash git clone https://github.com/ZhantianXu/PISAD.git cd pisad/ ``` Compiling should be as easy as: ```bash ./configure && make ``` To install in a specified directory: ```bash ./configure --prefix=/PATH && make install ``` ## Usage ##### Stage1: SNP callng : First, we select a low-error-rate sequencing dataset as the target sample for rapid SNP calling. It supports multi-threaded processing. Example: ```bash ./run.sh -i /data/hg002.fastq.gz -m 0 ``` ```bash Required parameters: -i: Input files ( *.fastq or *.fastq.gz files) -m: Heterozygosity parameter (0 for <1.2%, 1 otherwise) Optional parameters: -k: kmer-size (default: 21) -t: thread (default: 8)" -o: Output prefix (defaults: first input file's prefix) -d1: Directory for dsk files (default: current directory) -d2: Directory for output plot (default: current directory) -d3: Directory for SNP output (default: current directory) -h: Show this help message Advanced optional parameters: -est: est_kmercov (default: Estimated by algorithm) -cutoff: cutoff threshold (defaults: 0.95) -het: Initial heterozygosity (defaults: 0/0.12) -rho: Initial rho value (defaults: 0.2) -setleft: Left boundary of the heterozygous region (defaults: Estimated by algorithm) -setright: Right boundary of the heterozygous region (defaults: Estimated by algorithm) ``` ##### Stage1: construct variant sketch: Next, we convert the called SNPs into a variant sketch. ```bash ./create -i /snp/hg002_21_2_4_pairex.snp ``` ```bash Required parameters: -i: Input files ( .snp file) Optional parameters: -k: kmer-size (default: 21) -l: Filtering threshold (default: 21) -o: Output prefix (defaults: current directory) ``` ##### Stage2: count the k-mers: we compare the k-mer counts of other cohort samples to the variant sketch to infer relationships between them. Files may be gzipped and multiple threads can be used. ```bash ./pisadCount -s /fa/hg002.fa /data/hg003.fastq.gz ``` ```bash Usage: ./pisadCount -s [FASTA] [OPTION]... [FILES...] Required options: -s: variant sketch (one or more) Optional options: -t: Number of threads to run (default: 1) -m: k-mer coverage threshold for early termination (default: inf) -i: extra debug information -k: k-mer size used (default: 21) -o: Evaluation file path (defaults: current directory) -h: Display this dialog ``` Here, the -s option allows inputting multiple FA files for variant sketching, separated by commas, such as `-s /fa/hg002.fa,/fa/hg001.fa`. If your input file has a high coverage, you can also add the `-m` parameter to control the reading process and save time, such as `-m 10`. ##### Stage2:Evaluate the samples: Input the statistics of samples to calculate their relationship and detect sample swaps. ```bash ./pisadEval /homeb/xuzt/coverage/eval/hg002_hg003.txt > summary.tsv ``` ```bash Usage: ./pisadEval [OPTION]... [FILES...] Optional options: -t: Number of threads to run(default: 1) -h: Display this dialog ```

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Main Workflow: PISAD - Phsaed Intraspecies Sample Anomalies Detection tool
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