maf-convert - Convert MAF-format alignments to tabular format
- maf-convert --help maf-convert axt mafFile(s) maf-convert bed
mafFile(s) maf-convert blast mafFile(s) maf-convert blasttab mafFile(s)
maf-convert chain mafFile(s) maf-convert gff mafFile(s) maf-convert html
mafFile(s) maf-convert psl mafFile(s) maf-convert sam mafFile(s)
maf-convert tab mafFile(s)
Read MAF-format alignments & write them in another format.
- -h, --help
- show this help message and exit
- -s N,
--subject=N
- which sequence to use as subject/reference
- -p, --protein
- assume protein alignments, for psl match counts
- -j N,
--join=N
- join consecutive co-linear alignments separated by <= N letters
- -J N,
--Join=N
- join nearest co-linear alignments separated by <= N letters
- -n,
--noheader
- omit any header lines from the output
- -d,
--dictionary
- include dictionary of sequence lengths in sam format
- -f DICTFILE,
--dictfile=DICTFILE
- get sequence dictionary from DICTFILE
- -r READGROUP,
--readgroup=READGROUP
- read group info for sam format
- -l LINESIZE,
--linesize=LINESIZE
- line length for blast and html formats (default: 60)