Convenience commands

In addition to the primary commands for the build, imputation, and resequencing pipelines, PHGv2 also provides a suite of "convenience commands" for miscellaneous "quality of life (QoL)" improvements. In this document, we will discuss the currently available external commands for performing highly used tasks.

Convert gVCF files to hVCF files

Create hVCF files from existing gVCF files created by the PHG

Command - gvcf2hvcf

Example

phg gvcf2hvcf \
    --bed my/bed/file.bed \
    --reference-file my/updated/ref/fasta.fa \
    --gvcf-dir gvcf/directory \
    --db-path my/phg/db

Parameters

Parameter name	Description	Default value	Required?
--bed	BED file with entries that define the haplotype boundaries.	""
--gvcf-dir	Directory containing bgzipped and CSI indexed gVCF files.	""
--reference-file	Path to local Reference FASTA file.	""
--conda-env-prefix	Prefix for the Conda environment to use. If provided, this should be the full path to the Conda environment.	Current active Conda environment
--db-path	Folder name where TileDB datasets and AGC record is stored. If not provided, the current working directory is used.	Current working dir

Convert hVCF files to gVCF files

Create gVCF files from existing hVCF files created by the PHG

Command - hvcf2gvcf

Example

phg hvcf2gvcf \
    --reference-file my/updated/ref/fasta.fa \
    --hvcf-dir hvcf/directory \
    --db-path my/phg/db
    --output-dir output/directory/for/gvcfs

Parameters

Parameter name	Description	Default value	Required?
--hvcf-dir	Path to directory holding hVCF files. Data will be pulled directly from these files instead of querying TileDB.	""
--reference-file	Path to local Reference FASTA file.	""
--conda-env-prefix	Prefix for the Conda environment to use. If provided, this should be the full path to the Conda environment.	Current active Conda environment
--db-path	Folder name where TileDB datasets and AGC record is stored. If not provided, the current working directory is used.	Current working dir
--output-dir	Output directory for the gVCF files. If not provided, the current working directory is used.	Current working dir

Merge gVCF files

Merge multiple gVCF files into a single gVCF file

Command - merge-gvcfs

Example

phg merge-gvcfs \
    --input-dir my/gvcf/directory \
    --output-file output/merged_gvcfs.g.vcf \

Parameters

Parameter name	Description	Default value	Required?
--input-dir	Path to input gVCF file directory.	""
--output-dir	Path and/or filename for merged gVCF file.	""

Merge hVCF files

Merge multiple hVCF files into a single hVCF file

Command - merge-hvcfs

Example

phg merge-hvcfs \
    --input-dir my/hvcf/directory \
    --output-file output/merged_hvcfs.h.vcf \
    --id-format CHECKSUM \
    --reference-file \
    --range-bedfile 

Parameters

Parameter name	Description	Default value	Required?
--input-dir	Path to input hVCF file directory.	""
--output-dir	Path and/or filename for merged hVCF file.	""
--id-format	ID format for hVCF files. Options are: CHECKSUM or RANGE_SAMPLE_GAMETE (see notes for further details).	RANGE_SAMPLE_GAMETE
--reference-file	Path to reference FASTA file.	""
--range-bedfile	Path to reference range BED file.	""

Note - id-fomat

If you select CHECKSUM for the --id-format parameter, the ID values will be MD5 checksums in the ##ALT header:

##ALT=<ID=06ae4e937668d301e325d43725a38c3f, ...>

If you select RANGE_SAMPLE_GAMETE, the ID values will change to a reference range/sample/gamete ID format:

##ALT=<ID=R000001_LineA_G01, ...>