diff --git a/Changelog.md b/Changelog.md
--- a/Changelog.md
+++ b/Changelog.md
@@ -1,3 +1,6 @@
+V 1.6.3: Pileup reference-base is read as upper case, even if it's not in the file.
+V 1.6.2: Made compatible with GHC 9 (thanks to github user sjakobi)
+
 V 1.6.0: Plink Output now supported.
 
 V 1.5.1.4: Plink BIM parsing now automatically converts from Numbers (0,1,2,3,4) to Letters (N,A,C,T,G).
diff --git a/sequence-formats.cabal b/sequence-formats.cabal
--- a/sequence-formats.cabal
+++ b/sequence-formats.cabal
@@ -1,6 +1,6 @@
 cabal-version:      >=1.10
 name:               sequence-formats
-version:            1.6.1
+version:            1.6.3
 license:            GPL-3
 license-file:       LICENSE
 maintainer:         stephan.schiffels@mac.com
diff --git a/src/SequenceFormats/FreqSum.hs b/src/SequenceFormats/FreqSum.hs
--- a/src/SequenceFormats/FreqSum.hs
+++ b/src/SequenceFormats/FreqSum.hs
@@ -7,7 +7,7 @@
 module SequenceFormats.FreqSum (readFreqSumStdIn, readFreqSumFile, FreqSumEntry(..),  
     FreqSumHeader(..), printFreqSumStdOut, printFreqSumFile, freqSumEntryToText) where
 
-import SequenceFormats.Utils (consumeProducer, Chrom(..))
+import SequenceFormats.Utils (consumeProducer, Chrom(..), readFileProd)
 
 import Control.Applicative ((<|>))
 import Control.Monad.Catch (MonadThrow, throwM)
@@ -73,7 +73,7 @@
 
 -- |A function to read a freqsum file from a file. Returns a pair of a freqSum Header and a Producer over all lines.
 readFreqSumFile :: (MonadSafe m) => FilePath -> m (FreqSumHeader, Producer FreqSumEntry m ())
-readFreqSumFile file = readFreqSumProd $ withFile file ReadMode PB.fromHandle
+readFreqSumFile = readFreqSumProd . readFileProd
 
 parseFreqSumHeader :: A.Parser FreqSumHeader
 parseFreqSumHeader = do
diff --git a/src/SequenceFormats/Pileup.hs b/src/SequenceFormats/Pileup.hs
--- a/src/SequenceFormats/Pileup.hs
+++ b/src/SequenceFormats/Pileup.hs
@@ -41,7 +41,7 @@
     _ <- A.space
     pos <- A.decimal
     _ <- A.space
-    refA <- A.satisfy (A.inClass "ACTGNactgnM")
+    refA <- toUpper <$> A.satisfy (A.inClass "ACTGNactgnM")
      -- for some reason, there is an M in the human reference at
      -- position 3:60830534 (both in hs37d5 and in hg19)
     _ <- A.space
diff --git a/src/SequenceFormats/Plink.hs b/src/SequenceFormats/Plink.hs
--- a/src/SequenceFormats/Plink.hs
+++ b/src/SequenceFormats/Plink.hs
@@ -100,7 +100,7 @@
 
 -- |A function to read a bed file from a file. Returns a Producer over all lines.
 readPlinkBedFile :: (MonadSafe m) => FilePath -> Int -> m (Producer GenoLine m ())
-readPlinkBedFile file nrInds = readPlinkBedProd nrInds (PS.withFile file ReadMode PB.fromHandle)
+readPlinkBedFile file nrInds = readPlinkBedProd nrInds (readFileProd file)
 
 -- |Function to read a Bim File from StdIn. Returns a Pipes-Producer over the EigenstratSnpEntries.
 readBimStdIn :: (MonadThrow m, MonadIO m) => Producer EigenstratSnpEntry m ()
diff --git a/src/SequenceFormats/RareAlleleHistogram.hs b/src/SequenceFormats/RareAlleleHistogram.hs
--- a/src/SequenceFormats/RareAlleleHistogram.hs
+++ b/src/SequenceFormats/RareAlleleHistogram.hs
@@ -93,7 +93,7 @@
 -- |Read a histogram from a File Handle.
 readHistogramFromHandle :: (MonadIO m) => Handle -> m RareAlleleHistogram
 readHistogramFromHandle handle = do
-    res <- evalStateT (parse parseHistogram) . PB.fromHandle $ handle
+    res <- evalStateT (parse parseHistogram) (PB.fromHandle handle)
     case res of
         Nothing -> throw (SeqFormatException "histogram file exhausted too early")
         Just (Left err) -> throw (SeqFormatException ("Histogram parsing error: " <> show err))
diff --git a/src/SequenceFormats/Utils.hs b/src/SequenceFormats/Utils.hs
--- a/src/SequenceFormats/Utils.hs
+++ b/src/SequenceFormats/Utils.hs
@@ -73,7 +73,7 @@
 consumeProducer parser prod = parsed parser prod >>= liftParsingErrors
 
 readFileProd :: (PS.MonadSafe m) => FilePath -> Producer B.ByteString m ()
-readFileProd f = PS.withFile f ReadMode PB.fromHandle
+readFileProd f = PS.withFile f ReadMode (\h -> PB.fromHandle h)
 
 word :: A.Parser B.ByteString
 word = A.takeTill isSpace
diff --git a/testDat/example.pileup b/testDat/example.pileup
--- a/testDat/example.pileup
+++ b/testDat/example.pileup
@@ -1,3 +1,3 @@
 1 1000 A 4 ..,C*. IIII 3 ..ac* III 8 ,,.,ccAA-3acccA IIIIIIII
-1 2000 C 4 ..C+4IIIIa IIII 3 ACt..* III 8 .a.a.C.C* IIIIIIII
+1 2000 c 4 ..C+4IIIIa IIII 3 ACt..* III 8 .a.a.C.C* IIIIIIII
 2 1000 G 4 ,,.,,..-3AccC*. IIII 3 .,,* III 8 .,,.,,* IIIIIIII