HLAminer is a software for HLA predictions from next-generation shotgun (NGS) sequence read data and supports direct read alignment and targeted de novo assembly of sequence reads.
java -jar cromwell.jar run hlaminer.wdl --inputs inputs.json
| Parameter | Value | Description |
|---|---|---|
fastqR1 |
File | Input file with the first mate reads. |
fastqR2 |
File | Input file with the second mate reads. |
outputFileNamePrefix |
String | Output prefix, customizable. Default is the first file's basename. |
| Parameter | Value | Default | Description |
|---|---|---|---|
runHlaMiner.jobMemory |
Int | 8 | Memory allocated to the task. |
runHlaMiner.timeout |
Int | 20 | Timeout in hours, needed to override imposed limits. |
runHlaMiner.hlaMiner |
String | "$HLAMINER_ROOT/bin/HLAminer.pl" | Path to the HLAminer.pl script |
runHlaMiner.hlaFasta |
String | "$HLAMINER_BWA_INDEX_ROOT/HLA-I_II_GEN.fasta" | Path to the reference fasta file |
runHlaMiner.pDesignationFile |
String | "$HLAMINER_BWA_INDEX_ROOT/HLAminer_v1.4/database/hla_nom_p.txt" | P-designation file, contains details of all HLA Sequences having the same antigen binding domains |
runHlaMiner.modules |
String | "hlaminer/1.4 hlaminer-bwa-index/0.7.17 bwa/0.7.17" | Names and versions of required modules. |
| Output | Type | Description |
|---|---|---|
resultFile |
File | Reporting alignment metrics |
logFile |
File | Log file with run info from HLAminer |
This section lists command(s) run by the hlaminer workflow
- Running hlaminer
hlaminer wraps HLAminer () tool in a cromwell workflow. HLAminer is used to profile the usage of HLA alleles in a sample. The tool works with sequence data of many types (ie. whole genome, whole transcriptome/RNA-Seq, exome), at the group and allele resolution. It supports predictions from a variety of DNA sequencing technologies including those from Illumina, MGI, PacBio and Oxford Nanopore.
The workflow takes fastq files as it's inputs and aligns using HLA-specific indexes using BWA (it is ran as a subworkflow). Below we have the command used to run HLAminer:
set -euo pipefail
bwa aln -e 0 -o 0 HLA_FASTA FASTQ1 > "ALIGNMENT1_SAI"
bwa aln -e 0 -o 0 HLA_FASTA FASTQ2 > "ALIGNMENT2_SAI"
bwa sampe -o 1000 HLA_FASTA "ALIGNEMNT1_SAI" "ALIGNMENT2_SAI" FASTQ1 FASTQ2 > "ALIGNMENT_SAM"
HLAMINER -a "ALIGNMENT_SAM" -h HLA_FASTA -p P_DESIGNATION_FILE -l OUTPUT_PREFIX
For support, please file an issue on the Github project or send an email to gsi@oicr.on.ca .
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