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 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)