How to specifiy sample paired normal control in snakemake pipeline

[TendoLiu]

Hi All, Maybe I missed something but are there a command in snakemake file to specify a sample-paired normal control in the snakemake file? I successfully run once in tumor only mode.

Thanks.

[gavinha]

Hi @TendoLiu

At the moment, paired tumor-normal analysis is not supported by the snakemake pipeline here. You can consider (TitanCNA)[https://github.com/gavinha/TitanCNA], which uses ichorCNA as a pre-processing step and does use tumor-normal pairing.

Specifically, the ichorCNA snakefile there handles it https://github.com/gavinha/TitanCNA/blob/master/scripts/snakemake/ichorCNA.snakefile

Hope this helps. Gavin

[TendoLiu]

Thanks Gavin. I was trying to modify the snakemake file by myself and this one confirmed I was not doing the wrong thing. BTW, I thought ichorCNA was optimized to run CNA analysis on cfDNA, but in fact it could be used for any CNA analysis?

Another, for the WIG file in inchorCNA, which version of hg19 genome was used as reference? I was overwhelmed by so many hg19 files.... For example: hg19_assembly=/bgfs/soesterreich/pan_data/soesterreich/Tendo/ReferenceFiles/hg19_Versions/Homo_sapiens_assembly19/Homo_sapiens_assembly19.fasta hg19_UCSC=/bgfs/soesterreich/pan_data/soesterreich/Tendo/ReferenceFiles/hg19_Versions/ucsc.hg19.fasta/ucsc.hg19.fasta hg19_v37=/bgfs/soesterreich/pan_data/soesterreich/Tendo/ReferenceFiles/hg19_Versions/human_g1k_v37.fasta/human_g1k_v37.fasta hg19_v37_decoy=/bgfs/soesterreich/pan_data/soesterreich/Tendo/ReferenceFiles/hg19_Versions/human_g1k_v37.fasta/human_g1k_v37_decoy.fasta hg19_UCSC_genomeFa=/bgfs/soesterreich/pan_data/soesterreich/Tendo/ReferenceFiles/hg19_Versions/UCSC_genome.fa/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa

I know BROAD institute prefer to call hg19 b37, but is it the one "human_g1k_v37.fasta" ? Your answer will be much appreciated.