alignments overlapping the specified regions will be output. An
alignment may be given multiple times if it is overlapping several
regions. A region can be presented, for example, in the following
-format: `chr2', `chr2:1000000' or `chr2:1,000,000-2,000,000'. The
-coordinate is 1-based.
+format: `chr2' (the whole chr2), `chr2:1000000' (region starting from
+1,000,000bp) or `chr2:1,000,000-2,000,000' (region between 1,000,000 and
+2,000,000bp including the end points). The coordinate is 1-based.
.B OPTIONS:
.RS
press `?' for help and press `g' to check the alignment start from a
region in the format like `chr10:10,000,000'.
-.RE
-
.TP
.B fixmate
samtools fixmate <in.nameSrt.bam> <out.bam>
.B ONLY
works with FR orientation and requires ISIZE is correctly set.
-.RE
-
.TP
.B rmdupse
samtools rmdupse <input.srt.bam> <out.bam>
Remove potential duplicates for single-ended reads. This command will
treat all reads as single-ended even if they are paired in fact.
-.RE
-
.TP
.B fillmd
samtools fillmd [-e] <aln.bam> <ref.fasta>