Update hpc scripts

Molmed · Mar 26, 2024 · 0bff528 · 0bff528
1 parent 14db34b
commit 0bff528
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Showing 2 changed files with 46 additions and 7 deletions.
diff --git a/01_hpc_processing/01_hpc_processing.sh b/01_hpc_processing/01_hpc_processing.sh
@@ -107,4 +107,25 @@ singularity exec jaffa-2.1.sif bpipe run \
 	    -p readLayout=single \
 	    -p refBase=REH_RnaSeq_HiFi_PacBio_IsoSeq_SMRT/jaffa/reference \
 	    /opt/JAFFA/JAFFAL.groovy \
-	    REH_RnaSeq_HiFi_PacBio_IsoSeq_SMRT/jaffa/*.fasta
+	    REH_RnaSeq_HiFi_PacBio_IsoSeq_SMRT/jaffa/*.fasta
+
+## SNV CALLING ON ILLUMINA WGS ##
+# GATK/4.3.0.0
+gatk Mutect2 \
+  -R hg38bundle/Homo_sapiens_assembly38.fasta \
+  -I fastq_data.md.bam \
+  --germline-resource af-only-gnomad.hg38.vcf.gz \
+  --panel-of-normals 1000g_pon.hg38.vcf.gz \
+  -O REH_SNV.vcf.gz
+
+gatk FilterMutectCalls \
+  -R hg38bundle/Homo_sapiens_assembly38.fasta \
+  -V REH_SNV.vcf.gz \
+  --unique-alt-read-count 2 \
+  --min-allele-fraction 0.3 \
+  -O REH_SNV.filtered.vcf.gz
+
+java -Xmx8g -jar snpEff.jar -v GRCh38.99 \
+	REH_SNV.filtered.vcf.gz > REH.mutect.filtered.ann.vcf.gz
+
+
diff --git a/01_hpc_processing/02_denovo_suppl.sh b/01_hpc_processing/02_denovo_suppl.sh
@@ -45,9 +45,27 @@ singularity exec minimap2.sif minimap2 \
 	    pb.ccs.merged.fastq.gz > \
 	    racon/mapping/pb.overlaps.sam
 
-# racon v1.5.0
-singularity exec racon.sif racon -t 48 \
-	    pb.ccs.merged.fastq.gz \
-	    racon/mapping/pb.overlaps.sam \
-	    flye/00-assembly/draft_assembly.fasta > \
-	    racon/mapping/assembly.racon.fasta
+### PHASING WITH HAPDU AND HAPDIFF ###
+singularity minimap2.sif minimap2 \
+	    -ax map-ont -t 30 \
+	    medaka/consensus.fasta \
+	    trimmed.merged.porechopped.fastq | \
+        singularity exec samtools.sif samtools sort -@ 4 -m 4G > \
+	    hapdup/ont_reads_to_flye_assembly.bam
+
+singularity exec samtools.sif samtools index -@ 4 \
+	    hapdup/ont_reads_to_flye_assembly.bam
+
+singularity exec --bind ./hapdup \
+	    hapdup.sif hapdup \
+	    --assembly medaka/consensus.fasta \
+	    --bam hapdup/ont_reads_to_flye_assembly.bam \
+	    --out-dir hapdup/out \
+	    -t 48 --rtype ont
+
+singularity exec --bind ./hapdiff \
+	    hapdiff.sif hapdiff.py \
+	    --reference hapdiff/hg38.fa \
+	    --pat hapdiff/hapdup_phased_1.fasta \
+	    --mat hapdiff/hapdup_phased_2.fasta \
+	    --out-dir ./hapdiff \