diff --git a/src/hatchet/utils/phase_snps.py b/src/hatchet/utils/phase_snps.py
index 4ff6eec4..99deee4c 100644
--- a/src/hatchet/utils/phase_snps.py
+++ b/src/hatchet/utils/phase_snps.py
@@ -247,8 +247,8 @@ def liftover(self, infile, chromosome, outname, chain, refgen, ch):
         # e.g. small contigs variably present among the assemblies
 
         cmd1 = (
-            f'{self.picard} LiftoverVcf -I {infile} -O {tmpfile} -CHAIN {chain} -R {refgen} -REJECT {rejfile} '
-            '--WARN_ON_MISSING_CONTIG true'
+            f'{self.picard} LiftoverVcf I={infile} O={tmpfile} CHAIN={chain} R={refgen} REJECT={rejfile} '
+            'WARN_ON_MISSING_CONTIG=true'
         )
         # need to change 'chr' notation depending on liftover direction
         c = chromosome if not ch else f'chr{chromosome}'
diff --git a/src/hatchet/utils/run.py b/src/hatchet/utils/run.py
index 5344e795..9210b72f 100644
--- a/src/hatchet/utils/run.py
+++ b/src/hatchet/utils/run.py
@@ -158,8 +158,8 @@ def main(args=None):
                 f'{output}/phase/',
                 '-L',
             ]
-            + (['-N'] if config.genotype_snps.chr_notation else [])
             + glob.glob(f'{output}/snps/*.vcf.gz')
+            + (['-N'] if config.genotype_snps.chr_notation else [])
             + extra_args
         )