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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

show this help message and exit
which sequence to use as subject/reference
assume protein alignments, for psl match counts
join consecutive co-linear alignments separated by <= N letters
join nearest co-linear alignments separated by <= N letters
omit any header lines from the output
include dictionary of sequence lengths in sam format
get sequence dictionary from DICTFILE
read group info for sam format
line length for blast and html formats (default: 60)
February 2023 maf-convert 1447