Commit d5d0c44d authored by Pradat Yoann's avatar Pradat Yoann

add vcf2maf_overwrite option

parent 07aba00c
......@@ -27,7 +27,7 @@ DataFrame = pd.core.frame.DataFrame
def run_annotator(vcf_folder: str, vcf_file: str, col_normal: str, col_tumor: str, tumor_id: str, normal_id: str,
infos_n_reads: list, infos_other: list, vcf2maf: str, vep_folder: str, vep_data: str, fasta: str,
dt_folders: dict, dt_identifiers: dict=None, vep_custom: Union[str,list]=None,
vep_overwrite:bool=False):
vep_overwrite: bool=False, vcf2maf_overwrite: bool=False):
"""
Run the manual, vcf2maf and vep annotations on one VCF file and assemble.
......@@ -47,6 +47,8 @@ def run_annotator(vcf_folder: str, vcf_file: str, col_normal: str, col_tumor: st
list of sigles that need extraction
vcf2maf: str
path to the vcf2maf perl script
vcf2maf_overwrite: bool, optional.
set to True to overwrite any existing previous run of vcf2maf.
vep_folder: str
path to the folder where the vep command is
vep_data: str
......@@ -98,7 +100,8 @@ def run_annotator(vcf_folder: str, vcf_file: str, col_normal: str, col_tumor: st
tmp_folder = dt_folders["vcf2maf_tmp_folder"],
tumor_id = tumor_id,
normal_id = normal_id,
fasta = fasta
fasta = fasta,
overwrite = vcf2maf_overwrite
)
run_vep_annotator(
......
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