Minimap2: GFF output

[iminkin]

Hi,

Is there a straightforward way to convert PAF to GFF format?

[lh3]

Sorry. You have to write a converter by yourself. minimap2 won't support GFF output.

[gbdias]

For future googlers,

An option to convert spliced alignments from SAM/BAM to gff/gtf:

1. Align sequences and convert to BAM
   minimap2 -ax splice --cs target.fa query.fa | samtools sort -O BAM - > alignments.bam
2. Convert to BED12 using BEDtools
   bedtools bamtobed -bed12 -i alignments.bam > alignments.bed
3. Convert to genePred using UCSC tools
   bedToGenePred alignments.bed alignments.genepred
4. Convert to GTF2 using UCSC tools
   genePredToGtf "file" alignments.genepred alignments.gtf

• genePredToGtf has additional options that might be useful in specific use cases.
• All of these tools are available in Bioconda.