bqsr_recal.sh has Empty ref Variable

Sydney-Informatics-Hub / Fastq-to-BAM

Optimised pipeline to process whole genome sequence data from fastq to BAM on NCI Gadi

GNU General Public License v3.0

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bqsr_recal.sh has Empty ref Variable #25

Closed DarioS closed 12 months ago

DarioS commented 12 months ago

Instructions don't say to fill in ref before executing PBS driver script (only $dbsnp mentioned for non-human in make input script).

ref=
thousandG_indels=../Reference/Known_vars/Homo_sapiens_assembly38.known_indels.vcf
gold_standard_indels=../Reference/Known_vars/Mills_and_1000G_gold_standard.indels.hg38.vcf
dbsnp=../Reference/Known_vars/Homo_sapiens_assembly38.dbsnp138.vcf

calizilla commented 12 months ago

Hi Dario, The ref variable is automatically filled when you run and enter the required inputs to the create_project.sh setup script. This is why updating this variable is not within the README for bqsr_recal.sh. Kind regards Cali