From fc2c1eef87e102750a3e90ce7261d92d2fcdd10f Mon Sep 17 00:00:00 2001 From: darrelln32 Date: Tue, 17 Sep 2024 09:46:27 -0400 Subject: [PATCH] Update LaunchMetrics.py adding option to use DRAGEN vcf file when aligning fastq data to human genome using DRAGEN --- scripts/LaunchMetrics.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/scripts/LaunchMetrics.py b/scripts/LaunchMetrics.py index 6f3c9f7..64e0e0d 100644 --- a/scripts/LaunchMetrics.py +++ b/scripts/LaunchMetrics.py @@ -176,11 +176,13 @@ def dragen(sample, run, sample_parameters, work_directory, dragen_directory, fas # get the correct path for the reference if (sample_parameters["GTAG"] == "GRCh38"): dragen_path = "/igo/work/igo/dragen_hash_tables/4.2/hg38-alt_masked.cnv.graph.hla.rna-9-r3.0-1" + vcfFileOption = "--qc-cross-cont-vcf /opt/edico/config/sample_cross_contamination_resource_hg38.vcf.gz" else: dragen_path = "/igo/work/igo/dragen_hash_tables/4.2/{}".format(sample_parameters["GTAG"]) + vcfFileOption = "" metric_file_prefix = "{}___P{}___{}___{}".format(run, sample.project[8:], sample.sample_id, sample_parameters["GTAG"]) - launch_dragen = "/opt/edico/bin/dragen --ref-dir {} --fastq-list {} --fastq-list-sample-id {} --intermediate-results-dir /staging/temp --output-directory {} --output-file-prefix {} --enable-sort true --enable-duplicate-marking true --bin_memory 50000000000".format(dragen_path, fastq_list, sample.sample_id, dragen_directory, sample.sample_id) + launch_dragen = "/opt/edico/bin/dragen --ref-dir {} --fastq-list {} --fastq-list-sample-id {} --intermediate-results-dir /staging/temp --output-directory {} --output-file-prefix {} --enable-sort true --enable-duplicate-marking true --bin_memory 50000000000 {}".format(dragen_path, fastq_list, sample.sample_id, dragen_directory, sample.sample_id, vcfFileOption) bsub_launch_dragen = "bsub -J {0}{1} -o {0}{1}.out -cwd \"{2}\" -m \"id01 id02 id03\" -q dragen -n 48 -M 4 {3}".format(dragen_job_name_header, sample.sample_id, dragen_directory, launch_dragen) print(bsub_launch_dragen) call(bsub_launch_dragen, shell = True)