From e68c561374b8de848d9b8345a07f15740705de07 Mon Sep 17 00:00:00 2001 From: Mariya Lysenkova Date: Tue, 26 Mar 2024 14:47:49 +0100 Subject: [PATCH] Add deepvariant hpc scripts --- 01_hpc_processing/01_hpc_processing.sh | 39 ++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/01_hpc_processing/01_hpc_processing.sh b/01_hpc_processing/01_hpc_processing.sh index f1b2f75..a76a30d 100644 --- a/01_hpc_processing/01_hpc_processing.sh +++ b/01_hpc_processing/01_hpc_processing.sh @@ -129,3 +129,42 @@ java -Xmx8g -jar snpEff.jar -v GRCh38.99 \ REH_SNV.filtered.vcf.gz > REH.mutect.filtered.ann.vcf.gz +# SNV CALLING FOR VAF PLOTS USING DEEPVARIANT ## +singularity exec --bind /usr/lib/locale/ \ + pepper_deepvariant_r0.8.sif \ + run_pepper_margin_deepvariant call_variant \ + -b ont.sorted.bam \ + -f hg38.fa \ + -o out \ + -p ONT_pepper \ + -t 30 \ + --ont_r9_guppy5_sup + +singularity exec \ + --bind deepvariant_input:/input \ + --bind deepvariant_output/illumina:/output \ + --bind reference/:/reference \ + deepvariant_latest.sif \ + /opt/deepvariant/bin/run_deepvariant \ + --model_type WGS \ + --ref /reference/Homo_sapiens_assembly38.fasta \ + --reads /input/fastq_data.recal.bam \ + --output_vcf /output/REH-illumina.output.vcf.gz \ + --output_gvcf /output/REH-illumina.output.g.vcf.gz \ + --num_shards 16 \ + --intermediate_results_dir /output/intermediate_results + + singularity exec \ + --bind deepvariant_input:/input \ + --bind deepvariant_output/illumina:/output \ + --bind reference/:/reference \ + deepvariant_latest.sif \ + /opt/deepvariant/bin/run_deepvariant \ + --model_type PACBIO \ + --ref /reference/hg38.fa \ + --reads /input/pt_004_hifi-mapped.bam \ + --output_vcf /output/REH-pacbio.output.vcf.gz \ + --output_gvcf /output/REH-pacbio.output.g.vcf.gz \ + --num_shards 16 \ + --intermediate_results_dir /output/intermediate_results +