faster way to delly run

[Hriday Home Chowdhury]

I am presently executing the somatic structural variant (SV) calling pipeline on data from large no of  patients (e.g; 155). I've observed that processing one sample typically requires around two days. Therefore, extrapolating for all 155  patients, the analysis is estimated to consume a substantial amount of time. To expedite this process, I have attempted setting 'export OMP_NUM_THREADS=8'.
Here i attached the run script "
#!/bin/bash
export OMP_NUM_THREADS=8
#data_list="/path/173_T_N_bam.list"
ref_fasta="/path/Homo_sapiens_assembly38.fasta"
excl_tsv="/path/human.hg38.excl.tsv"

while read sample_id tumor_bam normal_bam; do
echo "$sample_id"
output_bcf="${sample_id}_sv.bcf"

delly call -x "$excl_tsv" -o "$output_bcf" -g "$ref_fasta" "$tumor_bam" "$normal_bam"

done < $1

echo "Delly call completed for all patients in $data_list""
please help me . I want this high speed . How to do this in short time ?

[tr]

In general, it's better to run multiple patients in parallel instead of trying to run delly with more threads on a single patient. For delly, the number of threads should be always <= number of BAMs so for a matched tumor-normal cancer genomics sample I would recommend to use " export OMP_NUM_THREADS=2"