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>