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Filtering VCF files

The filter script: vcf_filter.py

Filtering a VCF file based on some properties of interest is a common enough operation that PyVCF offers an extensible script. vcf_filter.py does the work of reading input, updating the metadata and filtering the records.

Existing Filters

.. autoclass:: vcf.filters.SiteQuality

.. autoclass:: vcf.filters.VariantGenotypeQuality

.. autoclass:: vcf.filters.ErrorBiasFilter

.. autoclass:: vcf.filters.DepthPerSample

.. autoclass:: vcf.filters.AvgDepthPerSample

.. autoclass:: vcf.filters.SnpOnly




Adding a filter

You can reuse this work by providing a filter class, rather than writing your own filter. For example, lets say I want to filter each site based on the quality of the site. I can create a class like this:

import vcf.filters
class SiteQuality(vcf.filters.Base):
    'Filter sites by quality'

    name = 'sq'

    @classmethod
    def customize_parser(self, parser):
        parser.add_argument('--site-quality', type=int, default=30,
                help='Filter sites below this quality')

    def __init__(self, args):
        self.threshold = args.site_quality

    def __call__(self, record):
        if record.QUAL < self.threshold:
            return record.QUAL

This class subclasses vcf.filters.Base which provides the interface for VCF filters. The docstring and name are metadata about the parser. The docstring provides the help for the script, and the first line is included in the FILTER metadata when applied to a file.

The customize_parser method allows you to add arguments to the script. We use the __init__ method to grab the argument of interest from the parser. Finally, the __call__ method processes each record and returns a value if the filter failed. The base class uses the name and threshold to create the filter ID in the VCF file.

To make vcf_filter.py aware of the filter, you can either use the local script option or declare an entry point. To use a local script, simply call vcf_filter:

$ vcf_filter.py --local-script my_filters.py ...

To use an entry point, you need to declare a vcf.filters entry point in your setup:

setup(
    ...
    entry_points = {
        'vcf.filters': [
            'site_quality = module.path:SiteQuality',
        ]
    }
)

Either way, when you call vcf_filter.py, you should see your filter in the list of available filters:

usage: vcf_filter.py [-h] [--no-short-circuit] [--no-filtered]
              [--output OUTPUT] [--local-script LOCAL_SCRIPT]
              input filter [filter_args] [filter [filter_args]] ...


Filter a VCF file

positional arguments:
  input                 File to process (use - for STDIN) (default: None)

optional arguments:
  -h, --help            Show this help message and exit. (default: False)
  --no-short-circuit    Do not stop filter processing on a site if any filter
                        is triggered (default: False)
  --output OUTPUT       Filename to output [STDOUT] (default: <open file
                        '<stdout>', mode 'w' at 0x1002841e0>)
  --no-filtered         Output only sites passing the filters (default: False)
  --local-script LOCAL_SCRIPT
                        Python file in current working directory with the
                        filter classes (default: None)

sq:
  Filter sites by quality

  --site-quality SITE_QUALITY
                        Filter sites below this quality (default: 30)

The filter base class: vcf.filters.Base

.. autoclass:: vcf.filters.Base
   :members:



Utilities

.. automodule:: vcf.utils

Simultaneously iterate two or more files

.. autofunction:: vcf.utils.walk_together

Trim common suffix

.. autofunction:: vcf.utils.trim_common_suffix


vcf_melt

This script converts a VCF file from wide format (many calls per row) to a long format (one call per row). This is useful if you want to grep per sample or for really quick import into, say, a spreadsheet:

$ vcf_melt < vcf/test/gatk.vcf
SAMPLE      AD      DP      GQ      GT      PL      FILTER  CHROM   POS     REF     ALT     ID      info.AC info.AF info.AN info.BaseQRankSum       info.DB info.DP info.DS info.Dels       info.FS info.HRun       info.HaplotypeScore     info.InbreedingCoeff    info.MQ info.MQ0        info.MQRankSum  info.QD info.ReadPosRankSum
BLANK       6,0     6       18.04   0/0     0,18,211        .       chr22   42522392        G       [A]     rs28371738      2       0.143   14      0.375   True    1506    True    0.0     0.0     0       123.5516                253.92  0       0.685   5.9     0.59
NA12878     138,107 250     99.0    0/1     1961,0,3049     .       chr22   42522392        G       [A]     rs28371738      2       0.143   14      0.375   True    1506    True    0.0     0.0     0       123.5516                253.92  0       0.685   5.9     0.59
NA12891     169,77  250     99.0    0/1     1038,0,3533     .       chr22   42522392        G       [A]     rs28371738      2       0.143   14      0.375   True    1506    True    0.0     0.0     0       123.5516                253.92  0       0.685   5.9     0.59
NA12892     249,0   250     99.0    0/0     0,600,5732      .       chr22   42522392        G       [A]     rs28371738      2       0.143   14      0.375   True    1506    True    0.0     0.0     0       123.5516                253.92  0       0.685   5.9     0.59
NA19238     248,1   250     99.0    0/0     0,627,6191      .       chr22   42522392        G       [A]     rs28371738      2       0.143   14      0.375   True    1506    True    0.0     0.0     0       123.5516                253.92  0       0.685   5.9     0.59
NA19239     250,0   250     99.0    0/0     0,615,5899      .       chr22   42522392        G       [A]     rs28371738      2       0.143   14      0.375   True    1506    True    0.0     0.0     0       123.5516                253.92  0       0.685   5.9     0.59
NA19240     250,0   250     99.0    0/0     0,579,5674      .       chr22   42522392        G       [A]     rs28371738      2       0.143   14      0.375   True    1506    True    0.0     0.0     0       123.5516                253.92  0       0.685   5.9     0.59
BLANK       13,4    17      62.64   0/1     63,0,296        .       chr22   42522613        G       [C]     rs1135840       6       0.429   14      16.289  True    1518    True    0.03    0.0     0       142.5716                242.46  0       2.01    9.16    -1.731
NA12878     118,127 246     99.0    0/1     2396,0,1719     .       chr22   42522613        G       [C]     rs1135840       6       0.429   14      16.289  True    1518    True    0.03    0.0     0       142.5716                242.46  0       2.01    9.16    -1.731
NA12891     241,0   244     99.0    0/0     0,459,4476      .       chr22   42522613        G       [C]     rs1135840       6       0.429   14      16.289  True    1518    True    0.03    0.0     0       142.5716                242.46  0       2.01    9.16    -1.731
NA12892     161,85  246     99.0    0/1     1489,0,2353     .       chr22   42522613        G       [C]     rs1135840       6       0.429   14      16.289  True    1518    True    0.03    0.0     0       142.5716                242.46  0       2.01    9.16    -1.731
NA19238     110,132 242     99.0    0/1     2561,0,1488     .       chr22   42522613        G       [C]     rs1135840       6       0.429   14      16.289  True    1518    True    0.03    0.0     0       142.5716                242.46  0       2.01    9.16    -1.731
NA19239     106,135 242     99.0    0/1     2613,0,1389     .       chr22   42522613        G       [C]     rs1135840       6       0.429   14      16.289  True    1518    True    0.03    0.0     0       142.5716                242.46  0       2.01    9.16    -1.731
NA19240     116,126 243     99.0    0/1     2489,0,1537     .       chr22   42522613        G       [C]     rs1135840       6       0.429   14      16.289  True    1518    True    0.03    0.0     0       142.5716                242.46  0       2.01    9.16    -1.731
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