Return to Question

I have a bunch of PAF files resulting from the alignments of fastq files on a reference genome with minimap2. I would like to convert them into SAM/BAM format so I can use samtools mpileup to recover the read coverage at filtered positions

So far I've looked at paftools.js and found sam2paf but no paf2sam

I am open to suggestions but I'd like to avoid mapping the reads again.

I have a bunch of PAF files resulting from the alignments of fastq files on a reference genome with minimap2. I would like to convert them into SAM/BAM format so I can use samtools mpileup to recover the read coverage at filtered positions

So far I've looked at paftools.js and found sam2paf but no paf2sam

I am open to suggestions but I'd like to avoid mapping the reads again.

Edit

I have opened an issue on minimap2's github

Answer from Heng Li :

You need to rerun alignment. No tools exist to convert paf to sam.

why there is no paf2sam in paftools.js

It is technically possible, but someone needs to write the code.

I have a bunch of PAF files resulting from the alignments of fastq files on a reference genome with minimap2. I would like to convert them into SAM/BAM format so I can use samtools mpileup to recover the read coverage at filtered positions

So far I've looked at paftools.js and found sam2paf but no paf2sam

I am open to suggestions but I'd like to avoid mapping the reads again.

I have a bunch of PAF files resulting from the alignments of fastq files on a reference genome with minimap2. I would like to convert them into SAM/BAM format so I can use samtools mpileup to recover the read coverage at filtered positions

So far I've looked at paftools.js and found sam2paf but no paf2sam

I am open to suggestions but I'd like to avoid mapping the reads again.