diff --git a/src/main/java/htsjdk/samtools/reference/FastaReferenceWriter.java b/src/main/java/htsjdk/samtools/reference/FastaReferenceWriter.java
index 3ef6ecaa36..2bba48953c 100644
--- a/src/main/java/htsjdk/samtools/reference/FastaReferenceWriter.java
+++ b/src/main/java/htsjdk/samtools/reference/FastaReferenceWriter.java
@@ -174,8 +174,8 @@ public final class FastaReferenceWriter implements AutoCloseable {
      * <p>
      * You can specify a specific output stream to each file: the main fasta output, its index and its dictionary.
      * You can only provide a compressed stream to the fastaOutput, and only in the case that an index isn't written.
-     *
-     *
+     * <p>
+     * <p>
      * </p>
      *
      * @param fastaOutput the output fasta file path.
diff --git a/src/main/java/htsjdk/samtools/reference/FastaReferenceWriterBuilder.java b/src/main/java/htsjdk/samtools/reference/FastaReferenceWriterBuilder.java
index 629705947d..5ada299eb4 100644
--- a/src/main/java/htsjdk/samtools/reference/FastaReferenceWriterBuilder.java
+++ b/src/main/java/htsjdk/samtools/reference/FastaReferenceWriterBuilder.java
@@ -46,7 +46,7 @@ protected static int checkBasesPerLine(final int value) {
     }
 
     /**
-     * Set the output fasta file to write to.
+     * Set the output fasta file to write to. Doesn't (currently) support compressed filenames.
      * If the index file and output stream are both null and makeFaiOutput is true (default), a default index file will be created as well.
      * If the dictionary file and output stream are both null and makeDictOutput is true (default), a default dictionary file will be created as well.
      *
@@ -62,7 +62,7 @@ public FastaReferenceWriterBuilder setFastaFile(Path fastaFile) {
     }
 
     /**
-     * Set the output fasta file to write to.
+     * Set the output fasta file to write to. Doesn't (currently) support compressed filenames.
      * If the index file and output stream are both null and makeFaiOutput is true (default), a default index file will be created as well.
      * If the dictionary file and output stream are both null and makeDictOutput is true (default), a default dictionary file will be created as well.
      *
@@ -112,7 +112,7 @@ public FastaReferenceWriterBuilder setBasesPerLine(int basesPerLine) {
     }
 
     /**
-     * Set the output index file to write to.
+     * Set the output index file to write to. Doesn't (currently) support compressed filenames.
      */
     public FastaReferenceWriterBuilder setIndexFile(Path indexFile) {
         this.indexFile = indexFile;
@@ -121,7 +121,7 @@ public FastaReferenceWriterBuilder setIndexFile(Path indexFile) {
     }
 
     /**
-     * Set the output index file to write to.
+     * Set the output index file to write to. Doesn't (currently) support compressed filenames.
      */
     public FastaReferenceWriterBuilder setIndexFile(File indexFile) {
         return setIndexFile(indexFile.toPath());
@@ -137,14 +137,14 @@ public FastaReferenceWriterBuilder setDictFile(Path dictFile) {
     }
 
     /**
-     * Set the output dictionary file to write to.
+     * Set the output dictionary file to write to. Doesn't (currently) support compressed filenames.
      */
     public FastaReferenceWriterBuilder setDictFile(File dictFile) {
         return setDictFile(dictFile.toPath());
     }
 
     /**
-     * Set the output stream for writing the reference.
+     * Set the output stream for writing the reference. Doesn't support compressed streams.
      *
      * @param fastaOutput a {@link OutputStream} for the output fasta file.
      * @return this builder
@@ -157,7 +157,7 @@ public FastaReferenceWriterBuilder setFastaOutput(OutputStream fastaOutput) {
     }
 
     /**
-     * Set the output stream for writing the index.
+     * Set the output stream for writing the index. Doesn't support compressed streams.
      *
      * @param indexOutput a  {@link OutputStream} for the output index.
      * @return this builder
@@ -169,7 +169,7 @@ public FastaReferenceWriterBuilder setIndexOutput(OutputStream indexOutput) {
     }
 
     /**
-     * Set the output stream for writing the dictionary.
+     * Set the output stream for writing the dictionary. Doesn't support compressed streams.
      *
      * @param dictOutput a {@link OutputStream} for the output dictionary.
      * @return this builder