table of contents
| MAF-CONVERT(1) | User Commands | MAF-CONVERT(1) |
NAME¶
maf-convert - Convert MAF-format alignments to tabular format
DESCRIPTION¶
Usage:¶
- 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.
OPTIONS¶
- -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)
| August 2024 | maf-convert 1542 |