# PPP 0.1.13
{{< admonition success "Installed" true >}}
This software should be available with no extra configuration.
{{< /admonition >}}
## ppp-0.1.13 - Popgen Pipeline Platform (PPP)
The PPP is a software platform with the goal of reducing the computational
expertise required for conducting population genomic analyses. The PPP was
designed as a collection of scripts that facilitate common population genomic
workflows in a consistent and standardized environment. Functions were
developed to encompass entire workflows, including: input preparation, file
format conversion, various population genomic analyses, output generation, and
visualization. By facilitating entire workflows, the PPP offers several
benefits to prospective end users - it reduces the need of redundant in-house
software and scripts that would require development time and may be
error-prone, or incorrect, depending on the expertise of the investigator. The
platform has also been developed with reproducibility and extensibility of
analyses in mind.
The current documentation may be found [here](https://ppp.readthedocs.io/).
A PDF of the documentation is also available for
[download](https://readthedocs.org/projects/ppp/downloads/pdf/latest/).
-------------------------------------------------------------------------------
## Location and version
```console
$ which vcf_filter.py
/local/cluster/bin/vcf_filter.py
$ vcf_filter.py -h
initLogger - WARNING: PPP, version 0.1.13
```
## help message
There are other scripts associated with this software as well.
Please see the full documentation for more information.
```console
$ vcf_filter.py -h
initLogger - WARNING: PPP, version 0.1.13
usage: vcf_filter.py [-h] --vcf VCF [--model-file MODEL_FILE] [--model MODEL]
[--out OUT] [--out-prefix OUT_PREFIX]
[--out-format {vcf, vcf.gz, bcf, bed, sites}]
[--overwrite] [--force-samples]
[--filter-include-indv FILTER_INCLUDE_INDV [FILTER_INCLUDE_INDV ...]
| --filter-exclude-indv FILTER_EXCLUDE_INDV
[FILTER_EXCLUDE_INDV ...]]
[--filter-include-indv-file FILTER_INCLUDE_INDV_FILE | --filter-exclude-indv-file FILTER_EXCLUDE_INDV_FILE]
[--filter-only-biallelic]
[--filter-min-alleles FILTER_MIN_ALLELES]
[--filter-max-alleles FILTER_MAX_ALLELES]
[--filter-max-missing FILTER_MAX_MISSING | --filter-max-missing-count FILTER_MAX_MISSING_COUNT]
[--filter-include-indels | --filter-exclude-indels]
[--filter-include-snps | --filter-exclude-snps]
[--filter-include-pos FILTER_INCLUDE_POS [FILTER_INCLUDE_POS ...]]
[--filter-exclude-pos FILTER_EXCLUDE_POS [FILTER_EXCLUDE_POS ...]]
[--filter-include-pos-file FILTER_INCLUDE_POS_FILE]
[--filter-exclude-pos-file FILTER_EXCLUDE_POS_FILE]
[--filter-include-bed FILTER_INCLUDE_BED]
[--filter-exclude-bed FILTER_EXCLUDE_BED]
[--filter-include-passed] [--filter-exclude-passed]
[--filter-include-flag FILTER_INCLUDE_FLAG [FILTER_INCLUDE_FLAG ...]]
[--filter-exclude-flag FILTER_EXCLUDE_FLAG [FILTER_EXCLUDE_FLAG ...]]
[--filter-include-snp FILTER_INCLUDE_SNP [FILTER_INCLUDE_SNP ...]]
[--filter-exclude-snp FILTER_EXCLUDE_SNP [FILTER_EXCLUDE_SNP ...]]
[--filter-include-snp-file FILTER_INCLUDE_SNP_FILE]
[--filter-exclude-snp-file FILTER_EXCLUDE_SNP_FILE]
[--filter-maf-min FILTER_MAF_MIN]
[--filter-maf-max FILTER_MAF_MAX]
[--filter-mac-min FILTER_MAC_MIN]
[--filter-mac-max FILTER_MAC_MAX]
optional arguments:
-h, --help show this help message and exit
--vcf VCF Defines the filename of the VCF (default: None)
--model-file MODEL_FILE
Defines the model file (default: None)
--model MODEL Defines the model and the individual(s) to include
(default: None)
--out OUT Defines the complete output filename, overrides --out-
prefix (default: None)
--out-prefix OUT_PREFIX
Defines the output prefix (i.e. filename without file
extension) (default: out)
--out-format {vcf, vcf.gz, bcf, bed, sites}
Defines the desired output format (default: vcf.gz)
--overwrite Overwrite previous output (default: False)
--force-samples Ignore the error rasied when a sample that does not
exist (default: False)
--filter-include-indv FILTER_INCLUDE_INDV [FILTER_INCLUDE_INDV ...]
Defines the individual(s) to include. May be used
multiple times (default: None)
--filter-exclude-indv FILTER_EXCLUDE_INDV [FILTER_EXCLUDE_INDV ...]
Defines the individual(s) to exclude. May be used
multiple times (default: None)
--filter-include-indv-file FILTER_INCLUDE_INDV_FILE
Defines a file of individuals to include (default:
None)
--filter-exclude-indv-file FILTER_EXCLUDE_INDV_FILE
Defines a file of individuals to exclude (default:
None)
--filter-only-biallelic
Only include variants that are biallelic (default:
False)
--filter-min-alleles FILTER_MIN_ALLELES
Include variants with a number of allele >= to the
given number (default: None)
--filter-max-alleles FILTER_MAX_ALLELES
Include variants with a number of allele <= to the
given number (default: None)
--filter-max-missing FILTER_MAX_MISSING
Max proportion of missing data allowed (0.0: no
missing data, 1.0: include all data) (default: None)
--filter-max-missing-count FILTER_MAX_MISSING_COUNT
Max number of sample with missing data allowed
(default: None)
--filter-include-indels
Include variants if they contain an insertion or a
deletion (default: False)
--filter-exclude-indels
Exclude variants if they contain an insertion or a
deletion (default: False)
--filter-include-snps
Include variants if they contain a SNP (default:
False)
--filter-exclude-snps
Exclude variants if they contain a SNP (default:
False)
--filter-include-pos FILTER_INCLUDE_POS [FILTER_INCLUDE_POS ...]
Defines comma seperated positions (i.e. CHROM:START-
END) to include. START and END are optional. May be
used multiple times (default: None)
--filter-exclude-pos FILTER_EXCLUDE_POS [FILTER_EXCLUDE_POS ...]
Defines comma seperated positions (i.e. CHROM:START-
END) to exclude. START and END are optional. May be
used multiple times (default: None)
--filter-include-pos-file FILTER_INCLUDE_POS_FILE
Defines a file of positions to include within a file
(default: None)
--filter-exclude-pos-file FILTER_EXCLUDE_POS_FILE
Defines a file of positions to exclude within a file
(default: None)
--filter-include-bed FILTER_INCLUDE_BED
Defines a BED file of positions to include (default:
None)
--filter-exclude-bed FILTER_EXCLUDE_BED
Defines a BED file of positions to exclude (default:
None)
--filter-include-passed
Include variants with the 'PASS' filter flag (default:
False)
--filter-exclude-passed
Exclude variants with the 'PASS' filter flag (default:
False)
--filter-include-flag FILTER_INCLUDE_FLAG [FILTER_INCLUDE_FLAG ...]
Include variants with the specified filter flag
(default: None)
--filter-exclude-flag FILTER_EXCLUDE_FLAG [FILTER_EXCLUDE_FLAG ...]
Exclude variants with the specified filter flag
(default: None)
--filter-include-snp FILTER_INCLUDE_SNP [FILTER_INCLUDE_SNP ...]
Include SNP(s) with the matching ID. This argument may
be used multiple times (default: None)
--filter-exclude-snp FILTER_EXCLUDE_SNP [FILTER_EXCLUDE_SNP ...]
Exclude SNP(s) with the matching ID. This argument may
be used multiple times (default: None)
--filter-include-snp-file FILTER_INCLUDE_SNP_FILE
Defines a file of SNP IDs to include (default: None)
--filter-exclude-snp-file FILTER_EXCLUDE_SNP_FILE
Defines a file of SNP IDs to exclude (default: None)
--filter-maf-min FILTER_MAF_MIN
Include variants with equal or greater MAF values
(default: None)
--filter-maf-max FILTER_MAF_MAX
Include variants with equal or lesser MAF values
(default: None)
--filter-mac-min FILTER_MAC_MIN
Include variants with equal or greater MAC values
(default: None)
--filter-mac-max FILTER_MAC_MAX
Include variants with equal or lesser MAC values
(default: None)
```
software ref:
research ref: