* optionally drop phase ambiguous reads

[samtools.git] / samtools.1

diff --git a/samtools.1 b/samtools.1
index 8d299b78dc079b6961e14137324ecad32e4b66d0..f4a54f57cf3796581ab6f881f1957f5fc016d732 100644 (file)
--- a/samtools.1
+++ b/samtools.1
@@ -414,12 +414,15 @@ designed for cutting fosmid clones from fosmid pool sequencing [Ref. Kitzman et
 
 .TP
 .B phase
-samtools phase [-F] [-k len] [-b prefix] [-q minLOD] [-Q minBaseQ] <in.bam>
+samtools phase [-AF] [-k len] [-b prefix] [-q minLOD] [-Q minBaseQ] <in.bam>
 
 Call and phase heterozygous SNPs.
 .B OPTIONS:
 .RS
 .TP 8
+.B -A
+Drop reads with ambiguous phase.
+.TP 8
 .BI -b \ STR
 Prefix of BAM output. When this option is in use, phase-0 reads will be saved in file
 .BR STR .0.bam