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
I am open to suggestions but I'd like to avoid mapping the reads again.
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.
paf2sam. Could it be that the conversion in that direction isn't possible? Perhaps
pafis missing information that would be essential for sam? $\endgroup$
CIGARcan take different format depending on the
input/output options. It might also be not written in the PAF in some case. Is that CIGAR essential to sam ? $\endgroup$
minimap2is fast. Just add the
-aoption when you re-run, which outputs the alignment in