Issue with CS/MD Tags and secphase Output in pbmm2-Aligned BAM

[LuyaoRen]

Hi,

I used pbmm2 and minimap2 as the aligner, but I did not generate CS or MD tags.

I got MS tag using samtools without realignment

samtools calmd -b output.bam reference.fa > output_with_md.bam

After adding MD tags using samtools, I ran the following secphase command:

secphase --hifi -i sample.all.sorted.bam -f diploid_ref.fasta --outDir sample_CCS --prefix sample_CCS --threads 20

However, I ended up with empty output files, including:

sample_CCS.initial_variant_blocks.bed
sample_CCS.out.log
sample_CCS.modified_read_blocks.variants.bed
sample_CCS.modified_read_blocks.markers.bed
sample_CCS.variant_blocks.bed
sample_CCS.marker_blocks.bed

Could you advise on how to properly generate the required tags (CS, MD) for secphase to function correctly? And why the output files are empty, it ran without any errors?

Thanks

[hanqu24]

@LuyaoRen Hello, I’m encountering the same issue now. Have you found a way to resolve it? Thank you!