From 35856b3c276e2039ab992b61503e8751da93cd8f Mon Sep 17 00:00:00 2001 From: Ed Date: Mon, 7 May 2018 12:56:29 -0400 Subject: [PATCH] just fixing the fasta files --- analysis/MTvariantpipeline.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/analysis/MTvariantpipeline.py b/analysis/MTvariantpipeline.py index 8650509..5b8f012 100644 --- 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'