just fixing the fasta files

agorelick · May 7, 2018 · 35856b3 · 35856b3
1 parent 94ee4e0
commit 35856b3
Showing 1 changed file with 4 additions and 2 deletions.
diff --git a/analysis/MTvariantpipeline.py b/analysis/MTvariantpipeline.py
@@ -43,7 +43,8 @@
     maf2maf_fasta = fasta
     bcfploidy_genome = 'GRCh37'
 elif genome == 'GRCh38':
-    fasta = '/ifs/depot/assemblies/H.sapiens/GRCh38_GDC/GRCh38.d1.vd1.fa'
+    #fasta = '/ifs/depot/assemblies/H.sapiens/GRCh38_GDC/GRCh38.d1.vd1.fa'
+    fasta = '/ifs/depot/pi/resources/genomes/GRCh38/fasta/GRCh38.d1.vd1.fa'
     mtchrom = 'chrM'
     ncbibuild = 'GRCh38'
     maf2maf_fasta = fasta
@@ -59,7 +60,8 @@
     rcrsmapping = pd.read_csv('/home/reznik/work/mtimpact/import/Yoruba2rCRS.txt',header = 0,index_col = 0)
 
     # we also need to make sure maf2maf uses the correct hg38 fasta
-    maf2maf_fasta = '/ifs/depot/assemblies/H.sapiens/GRCh38_GDC/GRCh38.d1.vd1.fa'
+    #maf2maf_fasta = '/ifs/depot/assemblies/H.sapiens/GRCh38_GDC/GRCh38.d1.vd1.fa'
+    maf2maf_fasta = '/ifs/depot/pi/resources/genomes/GRCh38/fasta/GRCh38.d1.vd1.fa'
 
     # ploidy for bcftools same as GRCh37
     bcfploidy_genome = 'GRCh37'