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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