X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=samtools.1;h=cc421d4bc34fd53efa123b4630fcbccb4ca58708;hb=ac32543c12eac42f12e0c66b78c3d53211caeaab;hp=77b5a22f62b6233f513d5695ad98a61d5474cdff;hpb=3bedbd7fb801e7d0ffdedf2eb53dcce9ff08d31a;p=samtools.git

diff --git a/samtools.1 b/samtools.1
index 77b5a22..cc421d4 100644
--- a/samtools.1
+++ b/samtools.1
@@ -606,6 +606,9 @@ consider to apply
 .B -C50
 to
 .BR mpileup .
+SNP calling in this way also works for single sample and has the
+advantage of enabling more powerful filtering. The drawback is the lack
+of short indel calling, which may be implemented in future.
 
 .IP o 2
 Derive the allele frequency spectrum (AFS) on a list of sites from multiple individuals: