Add run_whamg.sh

Author: VJalili

src/bash_workflows/run_whamg.sh

@@ -0,0 +1,67 @@
+#!/bin/bash
+
+set -Eeuo pipefail
+
+cram_file=$1
+cram_index=$2
+sample_id=$3
+reference_fasta=$4
+reference_index=$5
+include_bed_file=$6
+primary_contigs_list=$7
+cpu_cores=${8:-4}
+
+
+chr_list=$(paste -s -d ',' "${primary_contigs_list}")
+
+# print some info that may be useful for debugging
+df -h
+echo "whamg $(whamg 2>&1 | grep Version)"
+
+# necessary for getting permission to read from google bucket directly
+export GCS_OAUTH_TOKEN=`gcloud auth application-default print-access-token`
+
+echo "Converting cram to bam ..."
+# covert cram to bam
+samtools view -b1@ ${cpu_cores} -T "${reference_fasta}" "${cram_file}" > sample.bam
+echo "Finished converting cram to bam."
+
+# index bam file
+samtools index -@ ${cpu_cores} sample.bam
+
+# ensure that index files are present in appropriate locations
+ln -s sample.bam.bai sample.bai
+if [ ! -e "${reference_fasta}.fai" ]; then
+  ln -s "${reference_index}" "${reference_fasta}.fai"
+fi
+
+# run whamg on all specified intervals
+mkdir tmpVcfs
+cd tmpVcfs
+awk 'BEGIN{FS=OFS="\t"}{printf("%07d\t%s\n",NR,$1":"$2"-"$3)}' ${include_bed_file} |\
+  while read -r line interval; do
+    vcfFile="$line.wham.vcf.gz"
+    whamg \
+        -c ${chr_list}" \
+        -x ${cpu_cores} \
+        -a "${reference_fasta}" \
+        -f ../sample.bam \
+        -r $interval \
+      | bgzip -c > $vcfFile
+    bcftools index -t $vcfFile
+  done
+
+# We need to update both the VCF sample ID and the TAGS INFO field in the WHAM output VCFs.
+# WHAM uses both to store the sample identifier, and by default uses the SM identifier from the BAM file.
+# We need to update both to reflect the potentially-renamed sample identifier used by the pipeline (sample_id) --
+# svtk standardize_vcf uses the TAGS field to identify the sample for WHAM VCFs.
+
+ls -1 *.wham.vcf.gz > vcf.list
+bcftools concat -a -Ov -f vcf.list | \
+  sed -e 's/^#CHROM\t.*/#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t${sample_id}/' -e 's/;TAGS=[^;]*;/;TAGS=${sample_id};/' | \
+  bgzip -c > "../${sample_id}.wham.vcf.gz"
+cd ..
+bcftools index -t "${sample_id}.wham.vcf.gz"
+
+df -h
+ls -l