pyvcf 中带的一个工具 比其他工具用着好些 其他filter我很信不过~~  自己写的功能又很有限 所以转投vcf_filter.py啦

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

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 0x2b0f9435c150>)
  --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 low quailty sites

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

dps:
  Threshold read depth per sample

  --depth-per-sample DEPTH_PER_SAMPLE
                        Minimum required coverage in each sample (default: 5)

avg-dps:
  Threshold average read depth per sample (read_depth / sample_count)

  --avg-depth-per-sample AVG_DEPTH_PER_SAMPLE
                        Minimum required average coverage per sample (default:
                        3)

eb:
  Filter sites that look like correlated sequencing errors. Some sequencing
  technologies, notably pyrosequencing, produce mutation hotspots where
  there is a constant level of noise, producing some reference and some
  heterozygote calls. This filter computes a Bayes Factor for each site by
  comparing the binomial likelihood of the observed allelic depths under: *
  A model with constant error equal to the MAF. * A model where each sample
  is the ploidy reported by the caller. The test value is the log of the
  bayes factor. Higher values are more likely to be errors. Note: this
  filter requires rpy2

  --eblr EBLR           Filter sites above this error log odds ratio (default:
                        -10)

snp-only:
  Choose only SNP variants

mgq:
  Filters sites with only low quality variants. It is possible to have a
  high site quality with many low quality calls. This filter demands at
  least one call be above a threshold quality.

  --genotype-quality GENOTYPE_QUALITY
                        Filter sites with no genotypes above this quality
                        (default: 50)

懒得翻译 自己看吧

by freemao

FAFU

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