Implementation using BWA-mem2

[desmodus1984]

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;

[tahashmi]

Hi,

Sorry for late reply. bwa-mem support is here. Yes, you can use, but you have to do some changes in bwa-mem2 base code. Let me know, if you are still interested, I will guide you on them.