Added GRIDSS 2.2.3 backport for adjusting the SC field to exclude loc…

…al assembly anchor

PapenfussLab/gridss#213

hmftools/gridss/do_run_gridss_2_2_3_postpurple_backport_pilot

@@ -0,0 +1,81 @@
+#!/bin/bash
+#
+# Adjusts the breakpoint position to match GRIDSS 2.1.0 calling positions
+#
+source do_run_gridss_lib
+
+export PATH=$base_path/tools/bedops_v2.4.30/:$PATH
+
+PICARD_JAR=$base_path/tools/picard-tools_v1.135/picard.jar
+libgridss=/data/common/repos/scripts/gridss/
+gridss_pon=/data/common/dbs/gridss/pon3792v1/
+
+original_vcf=$(find -L ${run_dir}/structuralVariants/gridss/*/ -type f -name *gridss.vcf.gz)
+raw_somatic_vcf=$(dirname ${original_vcf})/${tumor_sample}.gridss.somatic.vcf.gz
+full_vcf=$(dirname ${original_vcf})/${tumor_sample}.gridss.somatic.full.vcf.gz
+assembly_sv_bam=$assembly_bam.gridss.working/$(basename $assembly_bam).sv.bam
+out_dir=$(dirname $full_vcf)/breakpoint_position_backport
+
+if [ ! -d "$out_dir" ] ; then
+	echo "Missing backport directory $out_dir. This assembly from this directory is required."
+fi
+
+normal_bam=$out_dir/$(basename $normal_bam)
+tumor_bam=$out_dir/$(basename $tumor_bam)
+assembly_bam=$out_dir/$(basename $assembly_bam)
+somatic_vcf=$out_dir/$(basename $raw_somatic_vcf .gz)
+
+
+input_vcf=$1
+output_vcf=${input_vcf/.sv.ann.vcf.gz/.sv.ann2.vcf}
+unadjusted_vcf=${input_vcf/.sv.ann.vcf.gz/.sv.unadjusted.vcf}
+fixedSC_vcf=${input_vcf/.sv.ann.vcf.gz/.sv.fixedSC.vcf}
+input_gridss_decompressed=${input_vcf/.vcf.gz/.gridss.vcf}
+input_purple_decompressed=${input_vcf/.vcf.gz/.purple.vcf}
+
+gunzip -c $input_vcf | grep -v purple_ > $input_gridss_decompressed
+gunzip -c $input_vcf | grep -E "^#" > $input_purple_decompressed
+gunzip -c $input_vcf | grep purple_ >> $input_purple_decompressed
+
+gridss_jvm_args="
+	-ea
+	-Dsamjdk.create_index=true
+	-Dsamjdk.use_async_io_read_samtools=true
+	-Dsamjdk.use_async_io_write_samtools=true
+	-Dsamjdk.use_async_io_write_tribble=true
+	-Dsamjdk.buffer_size=2097152
+	-cp $gridss_jar "
+gridss_common_args="
+	TMP_DIR=$out_dir/tmp
+	WORKING_DIR=$out_dir
+	REFERENCE_SEQUENCE=$ref_genome "
+
+java -Xmx4G $gridss_jvm_args gridss.AllocateEvidence \
+	ALLOCATE_READS=false \
+	I=$normal_bam \
+	I=$tumor_bam \
+	ASSEMBLY=$assembly_bam \
+	INPUT_VCF=$input_gridss_decompressed \
+	OUTPUT_VCF=$fixedSC_vcf \
+	$gridss_common_args \
+	CONFIGURATION_FILE=$gridss_config_file \
+	WORKER_THREADS=$threads | exit 1
+
+java -jar $PICARD_JAR SortVcf \
+	I=$fixedSC_vcf \
+	I=$input_purple_decompressed \
+	O=$unadjusted_vcf
+
+# Need to feed back to R to adjust nominal homology call position back to match gridss_somatic_filter
+Rscript ${libgridss}/gridss_adjust_call_positions.R -i ${unadjusted_vcf} -o ${output_vcf} -s ${libgridss}
+mv ${output_vcf}.bgz ${output_vcf}.gz
+mv ${output_vcf}.bgz.tbi ${output_vcf}.gz.tbi
+rm $fixedSC_vcf $unadjusted_vcf $input_purple_decompressed $input_gridss_decompressed
+
+
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+