diff --git a/src/main/java/picard/sam/AbstractAlignmentMerger.java b/src/main/java/picard/sam/AbstractAlignmentMerger.java
index f9bd6ab31..7475b88fa 100644
--- a/src/main/java/picard/sam/AbstractAlignmentMerger.java
+++ b/src/main/java/picard/sam/AbstractAlignmentMerger.java
@@ -57,11 +57,7 @@
 import picard.PicardException;
 
 import java.io.File;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Optional;
+import java.util.*;
 
 /**
  * Abstract class that coordinates the general task of taking in a set of alignment information,
@@ -105,6 +101,8 @@
     private final SAMFileHeader header;
     private final List<String> attributesToRetain = new ArrayList<String>();
     private final List<String> attributesToRemove = new ArrayList<String>();
+    private Set<String> attributesToReverse = new TreeSet<>(SAMRecord.TAGS_TO_REVERSE);
+    private Set<String> attributesToReverseComplement = new TreeSet<>(SAMRecord.TAGS_TO_REVERSE_COMPLEMENT);
     protected final File referenceFasta;
     private final Integer read1BasesTrimmed;
     private final Integer read2BasesTrimmed;
@@ -327,6 +325,20 @@ public AbstractAlignmentMerger(final File unmappedBamFile, final File targetBamF
         this.unmappingReadsStrategy = unmappingReadsStrategy;
     }
 
+    /** Gets the set of attributes to be reversed on reads marked as negative strand. */
+    public Set<String> getAttributesToReverse() { return attributesToReverse; }
+
+    /** Sets the set of attributes to be reversed on reads marked as negative strand. */
+    public void setAttributesToReverse(Set<String> attributesToReverse) { this.attributesToReverse = attributesToReverse; }
+
+    /** Gets the set of attributes to be reverse complemented on reads marked as negative strand. */
+    public Set<String> getAttributesToReverseComplement() { return attributesToReverseComplement; }
+
+    /** Sets the set of attributes to be reverse complemented on reads marked as negative strand. */
+    public void setAttributesToReverseComplement(Set<String> attributesToReverseComplement) {
+        this.attributesToReverseComplement = attributesToReverseComplement;
+    }
+
     /** Allows the caller to override the maximum records in RAM. */
     public void setMaxRecordsInRam(final int maxRecordsInRam) {
         this.maxRecordsInRam = maxRecordsInRam;
@@ -788,11 +800,7 @@ protected void setValuesFromAlignment(final SAMRecord rec, final SAMRecord align
         // If it's on the negative strand, reverse complement the bases
         // and reverse the order of the qualities
         if (rec.getReadNegativeStrandFlag()) {
-            if(needsSafeReverseComplement) {
-                rec.reverseComplement();
-            } else {
-                rec.reverseComplement(true);
-            }
+            rec.reverseComplement(attributesToReverseComplement, attributesToReverse, !needsSafeReverseComplement);
         }
     }
 
diff --git a/src/main/java/picard/sam/MergeBamAlignment.java b/src/main/java/picard/sam/MergeBamAlignment.java
index 2ed07d872..c1011baf2 100644
--- a/src/main/java/picard/sam/MergeBamAlignment.java
+++ b/src/main/java/picard/sam/MergeBamAlignment.java
@@ -25,6 +25,7 @@
 
 import htsjdk.samtools.SAMFileHeader.SortOrder;
 import htsjdk.samtools.SAMProgramRecord;
+import htsjdk.samtools.SAMRecord;
 import htsjdk.samtools.SamPairUtil;
 import htsjdk.samtools.util.Log;
 import picard.PicardException;
@@ -35,9 +36,7 @@
 import picard.cmdline.programgroups.SamOrBam;
 
 import java.io.File;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
+import java.util.*;
 
 /**
  * A command-line tool to merge BAM/SAM alignment info from a third-party aligner with the data in an
@@ -154,6 +153,12 @@
             "  This overrides ATTRIBUTES_TO_RETAIN if they share common tags.")
     public List<String> ATTRIBUTES_TO_REMOVE = new ArrayList<String>();
 
+    @Option(shortName="RV", doc="Attributes on negative strand reads that need to be reversed.")
+    public Set<String> ATTRIBUTES_TO_REVERSE = new TreeSet<>(SAMRecord.TAGS_TO_REVERSE);
+
+    @Option(shortName="RC", doc="Attributes on negative strand reads that need to be reverse complemented.")
+    public Set<String> ATTRIBUTES_TO_REVERSE_COMPLEMENT = new TreeSet<>(SAMRecord.TAGS_TO_REVERSE_COMPLEMENT);
+
     @Option(shortName = "R1_TRIM",
             doc = "The number of bases trimmed from the beginning of read 1 prior to alignment")
     public int READ1_TRIM = 0;
@@ -268,6 +273,8 @@ protected int doWork() {
         merger.setMaxRecordsInRam(MAX_RECORDS_IN_RAM);
         merger.setKeepAlignerProperPairFlags(ALIGNER_PROPER_PAIR_FLAGS);
         merger.setIncludeSecondaryAlignments(INCLUDE_SECONDARY_ALIGNMENTS);
+        merger.setAttributesToReverse(ATTRIBUTES_TO_REVERSE);
+        merger.setAttributesToReverseComplement(ATTRIBUTES_TO_REVERSE_COMPLEMENT);
         merger.mergeAlignment(REFERENCE_SEQUENCE);
         merger.close();
 
diff --git a/src/test/java/picard/sam/MergeBamAlignmentTest.java b/src/test/java/picard/sam/MergeBamAlignmentTest.java
index f3a031e38..b0c22c997 100644
--- a/src/test/java/picard/sam/MergeBamAlignmentTest.java
+++ b/src/test/java/picard/sam/MergeBamAlignmentTest.java
@@ -213,6 +213,13 @@ else if (sam.getReadName().equals("both_reads_present_only_first_aligns") ||
                 throw new Exception("Unexpected read name: " + sam.getReadName());
             }
 
+            final boolean pos = !sam.getReadNegativeStrandFlag();
+            Assert.assertEquals(sam.getAttribute("aa"), pos ? "Hello" : "olleH");
+            Assert.assertEquals(sam.getAttribute("ab"), pos ? "ATTCGG" : "CCGAAT");
+            Assert.assertEquals(sam.getAttribute("ac"), pos ? new byte[] {1,2,3} : new byte[] {3,2,1});
+            Assert.assertEquals(sam.getAttribute("as"), pos ? new short[]{1,2,3} : new short[]{3,2,1});
+            Assert.assertEquals(sam.getAttribute("ai"), pos ? new int[]  {1,2,3} : new int[]  {3,2,1});
+            Assert.assertEquals(sam.getAttribute("af"), pos ? new float[]{1,2,3} : new float[]{3,2,1});
         }
 
         // Quick test to make sure the program record gets picked up from the file if not specified
@@ -1310,6 +1317,11 @@ private void doMergeAlignment(final File unmappedBam, final List<File> alignedBa
                                   final SAMFileHeader.SortOrder sortOrder,
                                   final AbstractAlignmentMerger.UnmappingReadStrategy unmappingReadStrategy) {
 
+        final List<String> tagsToRc  = new ArrayList<>(SAMRecord.TAGS_TO_REVERSE_COMPLEMENT);
+        final List<String> tagsToRev = new ArrayList<>(SAMRecord.TAGS_TO_REVERSE);
+        tagsToRc.add("ab");
+        tagsToRev.addAll(Arrays.asList("aa", "ac", "as", "ai", "af"));
+
         final List<String> args = new ArrayList<>(Arrays.asList(
                 "UNMAPPED_BAM=" + unmappedBam.getAbsolutePath(),
                 "ALIGNED_READS_ONLY=" + alignReadsOnly,
@@ -1362,6 +1374,12 @@ private void doMergeAlignment(final File unmappedBam, final List<File> alignedBa
         if (attributesToRetain != null) {
             args.add("ATTRIBUTES_TO_RETAIN=" + attributesToRetain);
         }
+        for (final String t : tagsToRc) {
+            args.add("ATTRIBUTES_TO_REVERSE_COMPLEMENT=" + t);
+        }
+        for (final String t : tagsToRev) {
+            args.add("ATTRIBUTES_TO_REVERSE=" + t);
+        }
         if (includeSecondary != null) {
             args.add("INCLUDE_SECONDARY_ALIGNMENTS=" + includeSecondary);
         }
diff --git a/testdata/picard/sam/unmapped.sam b/testdata/picard/sam/unmapped.sam
index b47ad2bff..eaf1337b1 100644
--- a/testdata/picard/sam/unmapped.sam
+++ b/testdata/picard/sam/unmapped.sam
@@ -1,12 +1,12 @@
 @HD	VN:1.0	SO:queryname
 @RG	ID:0	SM:Hi,Mom!	PL:ILLUMINA
-both_reads_align_clip_adapter	77	*	0	0	*	*	0	0	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
-both_reads_align_clip_adapter	141	*	0	0	*	*	0	0	NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA	&/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1	RG:Z:0
-both_reads_align_clip_marked	77	*	0	0	*	*	0	0	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0	XT:i:97
-both_reads_align_clip_marked	141	*	0	0	*	*	0	0	NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA	&/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1	RG:Z:0	XT:i:97
-both_reads_present_only_first_aligns	77	*	0	0	*	*	0	0	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
-both_reads_present_only_first_aligns	141	*	0	0	*	*	0	0	NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA	&/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1	RG:Z:0
-neither_read_aligns_or_present	77	*	0	0	*	*	0	0	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
-neither_read_aligns_or_present	141	*	0	0	*	*	0	0	NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA	&/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1	RG:Z:0
-read_2_too_many_gaps	77	*	0	0	*	*	0	0	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
-read_2_too_many_gaps	141	*	0	0	*	*	0	0	NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA	&/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1	RG:Z:0
+both_reads_align_clip_adapter	77	*	0	0	*	*	0	0	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0	aa:Z:Hello	ab:Z:ATTCGG	ac:B:c,1,2,3	as:B:s,1,2,3	ai:B:i,1,2,3	af:B:f,1,2,3
+both_reads_align_clip_adapter	141	*	0	0	*	*	0	0	NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA	&/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1	RG:Z:0	aa:Z:Hello	ab:Z:ATTCGG	ac:B:c,1,2,3	as:B:s,1,2,3	ai:B:i,1,2,3	af:B:f,1,2,3
+both_reads_align_clip_marked	77	*	0	0	*	*	0	0	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0	XT:i:97	aa:Z:Hello	ab:Z:ATTCGG	ac:B:c,1,2,3	as:B:s,1,2,3	ai:B:i,1,2,3	af:B:f,1,2,3
+both_reads_align_clip_marked	141	*	0	0	*	*	0	0	NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA	&/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1	RG:Z:0	XT:i:97	aa:Z:Hello	ab:Z:ATTCGG	ac:B:c,1,2,3	as:B:s,1,2,3	ai:B:i,1,2,3	af:B:f,1,2,3
+both_reads_present_only_first_aligns	77	*	0	0	*	*	0	0	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0	aa:Z:Hello	ab:Z:ATTCGG	ac:B:c,1,2,3	as:B:s,1,2,3	ai:B:i,1,2,3	af:B:f,1,2,3
+both_reads_present_only_first_aligns	141	*	0	0	*	*	0	0	NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA	&/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1	RG:Z:0	aa:Z:Hello	ab:Z:ATTCGG	ac:B:c,1,2,3	as:B:s,1,2,3	ai:B:i,1,2,3	af:B:f,1,2,3
+neither_read_aligns_or_present	77	*	0	0	*	*	0	0	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0	aa:Z:Hello	ab:Z:ATTCGG	ac:B:c,1,2,3	as:B:s,1,2,3	ai:B:i,1,2,3	af:B:f,1,2,3
+neither_read_aligns_or_present	141	*	0	0	*	*	0	0	NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA	&/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1	RG:Z:0	aa:Z:Hello	ab:Z:ATTCGG	ac:B:c,1,2,3	as:B:s,1,2,3	ai:B:i,1,2,3	af:B:f,1,2,3
+read_2_too_many_gaps	77	*	0	0	*	*	0	0	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0	aa:Z:Hello	ab:Z:ATTCGG	ac:B:c,1,2,3	as:B:s,1,2,3	ai:B:i,1,2,3	af:B:f,1,2,3
+read_2_too_many_gaps	141	*	0	0	*	*	0	0	NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA	&/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1	RG:Z:0	aa:Z:Hello	ab:Z:ATTCGG	ac:B:c,1,2,3	as:B:s,1,2,3	ai:B:i,1,2,3	af:B:f,1,2,3