From 363bddda424face0e861f9d8ff6b89e0038cfb9b Mon Sep 17 00:00:00 2001 From: MokaGuys Date: Mon, 16 Oct 2023 11:35:08 +0100 Subject: [PATCH] update to newer exome depth bed and PON --- automate_demultiplex_config.py | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/automate_demultiplex_config.py b/automate_demultiplex_config.py index e579fb4b..77b58179 100644 --- a/automate_demultiplex_config.py +++ b/automate_demultiplex_config.py @@ -277,11 +277,11 @@ ED_cnvcalling_path = "Apps/ED_cnv_calling_v1.2.0" ED_cnvcalling_instance_type = "mem1_ssd1_v2_x4" #VCP1 exome depth -ED_readcount_normals_VCP1_file= "project-ByfFPz00jy1fk6PjpZ95F27J:file-GZ47PPj0xygQ8z3z8yQK1qJF"#"Pan5134_normals_v1.0.0.RData" -ED_VCP1_readcount_BEDfile_pannum = "Pan5134_exomedepth.bed" +ED_readcount_normals_VCP1_file= "project-ByfFPz00jy1fk6PjpZ95F27J:file-GZYK6380f66PPy4kjzVQ7xj8"#"Pan5191_normals_v1.0.0.RData" +ED_VCP1_readcount_BEDfile_pannum = "Pan5191_exomedepth.bed" #VCP2 normals data file -ED_readcount_normals_VCP2_file="project-ByfFPz00jy1fk6PjpZ95F27J:file-GZ8ybG00bx11vq9fXP1j7QQK"#"Pan5132_normals_v1.0.0.RData" -ED_VCP2_readcount_BEDfile_pannum = "Pan5132_exomedepth.bed" +ED_readcount_normals_VCP2_file="project-ByfFPz00jy1fk6PjpZ95F27J:file-GZYbq400YG627Q12g1bbP440"#"Pan5188_normals_v1.0.0.RData" +ED_VCP2_readcount_BEDfile_pannum = "Pan5188_exomedepth.bed" #VCP3 normals data file ED_readcount_normals_VCP3_file=None#"Pan5149_normals_v1.0.0.RData" ED_VCP3_readcount_BEDfile_pannum = "Pan5149_exomedepth.bed" @@ -1035,7 +1035,7 @@ "sambamba_bedfile": "Pan5123dataSambamba.bed", "variant_calling_bedfile": "Pan5119data.bed", "polyedge": "MSH2", - "exome_depth_cnvcalling_BED": "Pan5160" # use R211 CNV bedfile + "exome_depth_cnvcalling_BED": "Pan5193" # use R211 CNV bedfile }, "Pan4130": { # VCP2 R211 polyposis (Viapath) "mokapipe": True, @@ -1047,7 +1047,7 @@ "sambamba_bedfile": "Pan5123dataSambamba.bed", "variant_calling_bedfile": "Pan5119data.bed", "polyedge": "MSH2", - "exome_depth_cnvcalling_BED": "Pan5160" + "exome_depth_cnvcalling_BED": "Pan5193" }, "Pan5186": { # VCP2 R414 APC (Viapath) "mokapipe": True, @@ -1507,7 +1507,7 @@ "variant_calling_bedfile": "Pan5119data.bed", "sambamba_bedfile": "Pan5123dataSambamba.bed", "polyedge": "MSH2", - "exome_depth_cnvcalling_BED": "Pan5160" # useR211 bedfile + "exome_depth_cnvcalling_BED": "Pan5193" # useR211 bedfile }, "Pan4820": { # VCP2 STG R211 "mokapipe": True, @@ -1521,7 +1521,7 @@ "variant_calling_bedfile": "Pan5119data.bed", "sambamba_bedfile": "Pan5123dataSambamba.bed", "polyedge": "MSH2", - "exome_depth_cnvcalling_BED": "Pan5160" + "exome_depth_cnvcalling_BED": "Pan5193" }, "Pan5185": { # VCP2 STG R414 "mokapipe": True,