added the phase command

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index d6e8213e51c2d9938d15ced14b4eee0ff3859610..2c333e8c668cb1a48464637d2e56e2e3984d7269 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -934,6 +934,7 @@ int bam_mpileup(int argc, char *argv[])
                fprintf(stderr, "         -A          use anomalous read pairs in SNP/INDEL calling\n");
                fprintf(stderr, "         -g          generate BCF output\n");
                fprintf(stderr, "         -u          do not compress BCF output\n");
+               fprintf(stderr, "         -E          extended BAQ for higher sensitivity but lower specificity\n");
                fprintf(stderr, "         -B          disable BAQ computation\n");
                fprintf(stderr, "         -D          output per-sample DP\n");
                fprintf(stderr, "         -S          output per-sample SP (strand bias P-value, slow)\n");