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Legacy Documentation - PHG Version 1

This section contains documentation for PHG version 1, which is no longer actively developed. It is preserved here for archival and historical reference only. If you are looking to use the Practical Haplotype Graph, please refer to the PHG v2 documentation, which reflects the current version of the software.

CreateHaplotype Key File

Specification:

The Keyfile is a tab-separated text file which is used to set up the alignment, HaplotypeCaller and GVCF Upload steps for the PHG CreateHaplotypes Scripts.

The PHG will process the following columns:

HeaderName Description Required
sample_name Name of the taxon to be processed. Yes
sample_description Short Description of the sample_name. No, if not specified, an empty description will be used
files Comma-separated list of file names to be processed. This file list should not have the full paths pre appended. But rather it needs just the file names. Yes
type Type of the files to be processed. PHG Currently Supports FASTQ, BAM or GVCF. Yes
chrPhased Are the Chromosomes Phased? This needs to be 'true' or 'false' Yes for GVCF type
genePhased Are the Genes Phased? This needs to be 'true' or 'false' Yes for GVCF type
phasingConf What is the confidence of the phasing? This needs to be between 0.0 and 1.0. If working with inbreds, this can be set close to 1.0. Yes for GVCF type
libraryID What is the library ID of the fastq files. This is only used if running BWA during CreateHaplotypesFromFastq.groovy Yes only for FASTQ type
gvcfServerPath remote server name or address, followed by semicolon, followed by path on server where gvcfs files will be stored. Yes if running with PHG version 1.0 or higher

Because the entries in the 'files' column are comma separated, the PHG can do the following depending on the type:

  • FASTQ : pairwise or single ended alignment using bwa mem.
  • BAM : Run GATK/Sentieon HaplotypeCaller on all the BAM files specified in the list to create a single GVCF.
  • GVCF : upload haplotypes for taxon with ploidy > 1. Each file in the list will create a new haplotype. If using Heterozygous material, we expect you to phase the GVCF file prior to running CreateHaplotypesFromGVCF.groovy.

Sample File:

Note this file has the "gvcfServerPath" column required for PHG version 1.0 and above, but not required for prior versions.

#!txt

sample_name     sample_description      files   type    chrPhased       genePhased      phasingConf     libraryID       gvcfServerPath
Ref     Ref line aligned        Ref_R1.fastq    FASTQ   true    true    .99     dummyLib1       localhost;/Users/lcj34/temp/gvcfRemote/
LineA   LineA line aligned      LineA_R1.fastq  FASTQ   true    true    .99     dummyLib1       localhost;/Users/lcj34/temp/gvcfRemote/
LineB   LineB line aligned      LineB_R1.fastq  FASTQ   true    true    .99     dummyLib1       localhost;/Users/lcj34/temp/gvcfRemote/
RefA1   RefA1 line aligned      RefA1_R1.fastq  FASTQ   true    true    .99     dummyLib1       localhost;/Users/lcj34/temp/gvcfRemote/
LineA1  LineA1 line aligned     LineA1_R1.fastq FASTQ   true    true    .99     dummyLib1       localhost;/Users/lcj34/temp/gvcfRemote/
LineB1  LineB1 line aligned     LineB1_R1.fastq FASTQ   true    true    .99     dummyLib1       localhost;/Users/lcj34/temp/gvcfRemote/

RefA1   RefA1 Aligned using BWA RefA1_dummyLib1_srt_dedup.bam   BAM     true    true    .99     null    localhost;/Users/lcj34/temp/gvcfRemote/
Ref     Ref Aligned using BWA   Ref_dummyLib1_srt_dedup.bam     BAM     true    true    .99     null    localhost;/Users/lcj34/temp/gvcfRemote/
LineB1  LineB1 Aligned using BWA        LineB1_dummyLib1_srt_dedup.bam  BAM     true    true    .99     null    localhost;/Users/lcj34/temp/gvcfRemote/
LineA   LineA Aligned using BWA LineA_dummyLib1_srt_dedup.bam   BAM     true    true    .99     null    localhost;/Users/lcj34/temp/gvcfRemote/
LineB   LineB Aligned using BWA LineB_dummyLib1_srt_dedup.bam   BAM     true    true    .99     null    localhost;/Users/lcj34/temp/gvcfRemote/
LineA1  LineA1 Aligned using BWA        LineA1_dummyLib1_srt_dedup.bam  BAM     true    true    .99     null    localhost;/Users/lcj34/temp/gvcfRemote/
RefA1   RefA1 Aligned using BWA RefA1_haplotype_caller_output_filtered.g.vcf.gz GVCF    true    true    .99     null    localhost;/Users/lcj34/temp/gvcfRemote/
Ref     Ref Aligned using BWA   Ref_haplotype_caller_output_filtered.g.vcf.gz   GVCF    true    true    .99     null    localhost;/Users/lcj34/temp/gvcfRemote/
LineB1  LineB1 Aligned using BWA        LineB1_haplotype_caller_output_filtered.g.vcf.gz        GVCF    true    true    .99     null    localhost;/Users/lcj34/temp/gvcfRemote/
LineA   LineA Aligned using BWA LineA_haplotype_caller_output_filtered.g.vcf.gz GVCF    true    true    .99     null    localhost;/Users/lcj34/temp/gvcfRemote/
LineB   LineB Aligned using BWA LineB_haplotype_caller_output_filtered.g.vcf.gz GVCF    true    true    .99     null    localhost;/Users/lcj34/temp/gvcfRemote/
LineA1  LineA1 Aligned using BWA        LineA1_haplotype_caller_output_filtered.g.vcf.gz        GVCF    true    true    .99     null    localhost;/Users/lcj34/temp/gvcfRemote/

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