Implementation using BWA-mem2

Hi,
I am interested in using your software for variant calling.
I looked through the code, but it seems to be for long-reads (no paired-end files).`
time srun -N 2 -n 2 /home/tahmad/hawk/new/pc/minimap2-chrms/minimap2 -t 128 **-ax map-ont -R** '@RG\tID:None\tSM:sample\tPL:Pacbio\tLB:sample\tPU:lane' /scratch-shared/tahmad/bio_data/reference/GRCh38_no_alt_analysis_set.fasta /scratch-shared/tahmad/bio_data/long/HG002/ONT/HG002.fastq > /scratch-shared/tahmad/bio_data/long/HG002/ONT/out.sam`

Is it possible to use bwa-mem2 instead of bwa-mem for faster mapping?

Could you provide an example of how to run bwa-mem2, or bwa-mem, with paired-end reads, or
can I provide the coordinate-sorted bam file?

Thanks;

The issue asks about integrating bwa-mem2 for paired-end reads. First, examine the existing mapping code to see how bwa-mem is called, likely in shell scripts or C wrappers. Check if the pipeline accepts coordinate-sorted BAM files as input. Look for configuration files or command-line arguments that specify the aligner. Determine what changes are needed to support bwa-mem2 and paired-end FASTQ inputs, then test with a small dataset.

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