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OtherFunctionalities.md

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Other SComatic functionalities

Computing the number of callable sites per cell type

python scripts/GetCallableSites/GetAllCallableSites.py --help
usage: GetAllCallableSites.py [-h] --infile INFILE --outfile OUTFILE
                              [--max_cov MAX_COV]
                              [--min_cell_types MIN_CELL_TYPES]

Script to calculate the number of callable sites per cell type

optional arguments:
  -h, --help            show this help message and exit
  --infile INFILE       Tsv file obtained by BaseCellCalling.step1.py to be
                        analysed
  --outfile OUTFILE     Out file prefix
  --max_cov MAX_COV     Maximum coverage to record in the callable sites
                        table. Greater values will be collapsed to the
                        provided one. [Default: 150]
  --min_cell_types MIN_CELL_TYPES
                        Minimum number of cell types with enough
                        coverage/cells at a site to be considered as a
                        callable [Default: 2]

Example: check here to see how to run this script with an example sample.

Computing the number of callable sites per single cell

python scripts/SitesPerCell/SitesPerCell.py --help
usage: SitesPerCell.py [-h] --bam BAM --ref REF [--infile INFILE]
                       [--min_ct1 MIN_CT1] [--min_ct2 MIN_CT2]
                       [--out_folder OUT_FOLDER] [--id ID] [--nprocs NPROCS]
                       [--bin BIN] [--min_dp MIN_DP] [--min_cc MIN_CC]
                       [--min_bq MIN_BQ] [--min_mq MIN_MQ] [--tmp_dir TMP_DIR]

Script to calculate the number of callable sites per unique cell

optional arguments:
  -h, --help            show this help message and exit
  --bam BAM             Tumor bam file to be analysed
  --ref REF             Reference genome. *fai must be available in the same
                        folder as reference
  --infile INFILE       Base calling file (obtained by
                        BaseCellCalling.step1.py)
  --min_ct1 MIN_CT1     Minimum number of cell types with enough reads to
                        consider a genomic site. Default = 2
  --min_ct2 MIN_CT2     Minimum number of cell types with enough unique cell
                        counts to consider a genomic site. Default = 2
  --out_folder OUT_FOLDER
                        Out folder
  --id ID               Prefix of out file. If provided, please use next
                        format: *.[cell_type] . Example: sample1.t_cell. If
                        not provided, it is taken from bam file
  --nprocs NPROCS       Number of processes [Default = 1]
  --bin BIN             Bin size for running the analysis [Default 50000]
  --min_dp MIN_DP       Minimum coverage to consider the genomic site. Default
                        = 5
  --min_cc MIN_CC       Minimum number of cells required to consider a genomic
                        site. Default = 5
  --min_bq MIN_BQ       Minimum base quality permited for the base counts.
                        Default = 20
  --min_mq MIN_MQ       Minimum mapping quality required to analyse read.
                        Default = 255
  --tmp_dir TMP_DIR     Temporary folder for tmp files

Example: check here to see how to run this script with an example sample.

Computing the genotype for each cell at the variant sites

python scripts/SingleCellGenotype/SingleCellGenotype.py --help
usage: SingleCellGenotype.py [-h] --bam BAM --infile INFILE --ref REF --meta
                             META [--out_file OUT_FILE] [--alt_flag {Alt,All}]
                             [--nprocs NPROCS] [--bin BIN] [--min_bq MIN_BQ]
                             [--min_mq MIN_MQ] [--tissue TISSUE]
                             [--tmp_dir TMP_DIR]

Script to get the alleles observed in each unique cell for the variant sites

optional arguments:
  -h, --help            show this help message and exit
  --bam BAM             Tumor bam file to be analysed
  --infile INFILE       Base calling file (obtained by
                        BaseCellCalling.step2.py), ideally only the PASS
                        variants
  --ref REF             Reference genome. *fai must be available in the same
                        folder as reference
  --meta META           Metadata with cell barcodes per cell type
  --out_file OUT_FILE   Out file
  --alt_flag {Alt,All}  Flag to search for cells carrying the expected alt
                        variant (Alt) or all cells independent of the alt
                        allele observed (All)
  --nprocs NPROCS       Number of processes [Default = 1]
  --bin BIN             Bin size for running the analysis [Default 50000]
  --min_bq MIN_BQ       Minimum base quality permited for the base counts.
                        Default = 30
  --min_mq MIN_MQ       Minimum mapping quality required to analyse read.
                        Default = 255
  --max_dp MAX_DP       Maximum number of reads per genomic site that are read by pysam pileup,
                        to save time and memory. Set this value to 0 to switch this filter off
                        (recommended for high-depth sequencing). [Default: 8000]
  --tissue TISSUE       Tissue of the sample
  --tmp_dir TMP_DIR     Temporary folder for tmp files

Example: check here to see how to run this script with an example sample.

Description of the output here

Computing the trinucleotide context background

python scripts/TrinucleotideBackground/TrinucleotideContextBackground.py --help
usage: TrinucleotideContextBackground.py [-h] --in_tsv IN_TSV --out_file
                                         OUT_FILE

Script to obtain trincucleotide context background

optional arguments:
  -h, --help           show this help message and exit
  --in_tsv IN_TSV      File listing the tsv files to be used for the
                       trinucleotide context background computation (files
                       obtained in BaseCellCalling.step1.py)
  --out_file OUT_FILE  Output file

Example: check here to see how to run this script with an example sample.

Computing germline genotypes for known variants in single-cell datasets

This script is developed to genotype known polymorphic sites in the single-cell data. It takes as input the output of step 4.1 of the SComatic tool (obtained by the BaseCellCalling.step1.py script) and produces, by default, a new TSV file (*GermlineCalls.SComatic.tsv) with the germline variant status per site and sample. If the --ethnicity Yes parameter is specified, it produces an extra TSV file (*GermlineCalls.SComatic.ethnicity.tsv) required for running other tools, such as scAI-SNP.

The commands for running this tool are as follows:

python scripts/GermlineGenotyper/GermlineGenotyper.py --help
usage: scripts/GermlineGenotyper/GermlineGenotyper.py [-h] --snp SNP --tsv TSV --prefix PREFIX
                                   [--min_reads MIN_READS]
                                   [--min_cells MIN_CELLS]
                                   [--min_cells_types_exp MIN_CELLS_TYPES_EXP]
                                   [--min_cov MIN_COV]
                                   [--min_total_cells MIN_TOTAL_CELLS]
                                   [--ethnicity {Yes,No}]

Script to call germline variants in a list of polymorphic sites

optional arguments:
  -h, --help            show this help message and exit
  --snp SNP             File with SNPs to check. Format: chr:pos:ref:alt
  --tsv TSV             TSV file obtained by the
                        BaseCellCalling/BaseCellCalling.step1.py script
  --prefix PREFIX       Prefix for the out files. Full path and prefix
                        recommended
  --min_reads MIN_READS
                        Minimum number of reads supporting the alternative
                        allele [Default = 3]
  --min_cells MIN_CELLS
                        Minimum number of cells harbouring the alternative
                        allele [Default = 3]
  --min_cells_types_exp MIN_CELLS_TYPES_EXP
                        Minimum number of cell types with enough expression to
                        get a calls [Default = 1]
  --min_cov MIN_COV     Minimum number of reads covering the variant site.
                        [Default = 5 ]
  --min_total_cells MIN_TOTAL_CELLS
                        Minimum number of cells with at least one read
                        covering the variant site. [Default = 5]
  --ethnicity {Yes,No}  Specify if ethnicity format file should be created.
                        [Default: No]