X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_plcmd.c;h=2c333e8c668cb1a48464637d2e56e2e3984d7269;hb=7251efa37992752a8cf62ff363da0ad5099937bd;hp=d6e8213e51c2d9938d15ced14b4eee0ff3859610;hpb=205b696ea778f5b7cfe70e5531bfe6583b5af333;p=samtools.git

diff --git a/bam_plcmd.c b/bam_plcmd.c
index d6e8213..2c333e8 100644
--- 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");