add calmd troubleshooting

maxibor · Nov 16, 2020 · 432f472 · 432f472
1 parent 38ddbc8
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diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -19,6 +19,7 @@ __ homepage_
    API
    CLI
    output
+   troubleshooting
 
 
 

diff --git a/docs/source/troubleshooting.md b/docs/source/troubleshooting.md
@@ -0,0 +1,11 @@
+# Troubleshooting
+
+## My alignment files don't have a MD tag
+
+You can use [samtools calmd](http://www.htslib.org/doc/samtools-calmd.html) to set the MD tag
+
+Example:
+
+```bash
+samtools calmd -b alignment.bam reference.fasta > aln.bam
+```
diff --git a/pydamage/cli.py b/pydamage/cli.py
@@ -53,7 +53,7 @@ def cli(no_args_is_help=True, **kwargs):
     Contact: <borry[at]shh.mpg.de>
     Homepage & Documentation: github.com/maxibor/pydamage
 
-    BAM: path to BAM/SAM/CRAM alignment file
+    BAM: path to BAM/SAM/CRAM alignment file. MD tags need to be set.
     """
     analyze(**kwargs)