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Importing-CSVs-into-GenomicsDB.md

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Preliminaries

  • You need libcsv while [[compiling|Compiling-GenomicsDB]].
  • License terms: We use libcsv to parse CSV files. libcsv is licensed under the GNU Library or Lesser General Public License version 2.0 (LGPLv2). So, if you are re-distributing binaries or object files, they may be subject to LGPLv2 terms. Please ensure that any binaries/object files you distribute are compliant with LGPLv2. You can disable libcsv usage by not setting the USE_LIBCSV and LIBCSV_DIR flags during compilation. However, your binaries/executables will not be able to import CSV files into TileDB.

CSV format

Given a variant call at a specific position in the genome for a particular CallSet/sample, the CSV file format supported by GenomicsDB contains one line describing the call. Essentially, each line in the CSV describes one cell in the TileDB array.

The exact format of the CSV is shown below:

 <row>,<begin_column>,<end_column>,<REF>,<concatenated_ALT>,<QUAL>,<FILTER_field_specification>[,<other_fields_specification>]

Fixed fields:

  • row (mandatory, type: int64): Row number in TileDB for this sample/CallSet
  • begin_column (mandatory, type: int64): Column in TileDB at which the variant call begins.
  • end_column (mandatory, type: int64): Column in TileDB at which the variant call ends (inclusive).
  • REF (mandatory, type:string): Reference allele at the given position.
  • concatenated_ALT (mandatory, type: string): Concatenated alternate alleles separated by the character '|'. For example, if a given call has two alternate alleles TAG and TG, then the concatenated string would be TAG|TG.
  • QUAL (optional, type: float): Represents the QUAL field in a VCF. It can be left empty implying that the value was missing for this call.
  • FILTER_field_specification (mandatory, type: variable length list of integers): Each element of the FILTER field list is an integer representing the FILTERs that this call failed (similar to how a BCF represents FILTERs). The first element of this field is an integer displaying the number of elements in the list. A value of 0 indicates that the list is empty.

Additional fields can be optionally specified

  • <other_fields_specification>: The format depends on the type of field:
    • String type fields (fixed or variable length strings): The field should contain the string - an empty token indicates that the field is missing.
    • Fixed length field (int or float): The field should contain exactly N elements where N is the length of the field (fixed constant). One or more tokens may be left empty to indicate that those elements are missing.
    • Variable length field (int or float): The first element of this field should be an integer denoting the number of elements in the field for this call. It should then be followed by the elements of this field. An empty or missing field can be specified by setting the first element (field length) to 0 - no other elements should follow an empty field.

Example

The following line contains 2 fields in addition to the fixed fields:

  • SB: Fixed length field of 4 integers

  • PL: Variable length field of integers

      2,1857210,1857210,G,A|T,894.77,0,,,,,6,923,0,599,996,701,1697

The line specifies the variant call for row id 2, beginning at column 1857210 and ending at 1857210. The REF allele is 'G' and the call has 2 alternate alleles 'A' and 'T' (SNVs). The QUAL value is 894.77 and there are no FILTERs specified (hence FILTER field length = 0). The SB field is missing - denoted by the 4 empty tokens. The PL field consists of 6 integers - the length appears first (since PL is a variable length field) followed by the elements [923,0,599,996,701,1697].

Special fields

  • GT is represented in the CSV as a variable length list of integers - each element of the list refers to the allele index (0 for reference allele, 1 for the first alternate allele and so on). The length of the list represents the ploidy of the sample/CallSet and must be specified in the CSV line (since GT is treated as a variable length list).

Organizing your data

  • All CSV files imported into a TileDB array must respect the number and order of fields as defined in the [[vid_mapping_file|Importing-VCF-data-into-GenomicsDB#fields-information]].
  • The import program cannot handle CSV files where 2 lines have the same value of row and begin_column - this restriction is similar to that imposed on [[loading VCFs|Importing-VCF-data-into-GenomicsDB#organizing-your-data]].
  • The import program cannot handle CSV files where 2 lines have overlapping column intervals for the same row id.
  • Other requirements are the same as described in the wiki page for [[importing VCF data|Importing-VCF-data-into-GenomicsDB#organizing-your-data]].

Information about CSVs for the import program

Information is passed to the import program through JSON files that are largely identical to [[those described for VCF import|Importing-VCF-data-into-GenomicsDB#information-about-vcfs-for-the-import-program]]. The only addition is in the [[callset_mapping_file|Importing-VCF-data-into-GenomicsDB#samplescallsets]].

{
    "callsets" : { 
        "HG00141" : {
            "row_idx" : 0,
            "idx_in_file": 0,
            "filename": "test_outputs/merged_java_alt3.list.csv"
        },
        "HG01530" : {
            "row_idx" : 1,
            "idx_in_file": 1,
            "filename": "test_outputs/merged_java_alt3.list.csv"
        },
        "HG01958" : {
            "row_idx" : 2,
            "idx_in_file": 0,
            "filename": "test_outputs/HG01958.csv"
        }
    }
    "sorted_csv_files" : [
        "test_outputs/HG01958.csv"
    ],
    "unsorted_csv_files" : [
        "test_outputs/merged_java_alt3.list.csv"
    ]
}

By default, the import program assumes all input files are VCFs. The files (file paths) listed under the fields sorted_csv_files and unsorted_csv_files are marked as CSV files. Sorted CSV files are assumed to be sorted in [[column-major order|Basic-TileDB-GenomicsDB-terminology]].

Unsorted CSV files are first sorted by invoking the GNU sort command internally. To import unsorted CSV files, you must have GNU coreutils installed in your system and the command sort in your PATH. The sorted CSV file is stored in a temporary directory - generally /tmp but can be set to a different location when launching the import program. The temporary directory must be large enough to store all the sorted CSV files and the user must have write permission to the directory.

You can import a combination of CSVs and VCFs together as long as you list the CSVs correctly under sorted_csv_files and unsorted_csv_files.

Running the program

    ./bin/vcf2tiledb <loader_json>

Specifying a temporary directory to store sorted CSV files:

    ./bin/vcf2tiledb -T <tmp_directory> <loader_json>

You can use MPI to [[import data in parallel across nodes|Importing-VCF-data-into-GenomicsDB#running-the-program]].