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CCRGeneticsBranch / MeltzerLab_Nextflow_pipeline

MeltzerLab data processing Nextflow pipeline
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code for running NGSCheckMate #11

Open zhujack8 opened 11 months ago

zhujack8 commented 11 months ago

Run ngscheckmate_fastq to get vaf files:

`fq_str="fastq/T47D_BRCA1_Pg_7_20_23_L.BSB09421-1634_R1.fastq.gz fastq/T47D_BRCA1_Pg_7_20_23_L.BSB09421-1634_R2.fastq.gz" fq_str=${fq_str/ / -2 }

${NCM_HOME}/ngscheckmate_fastq -p $SLURM_CPUS_PER_TASK -1 $fq_str $NCM_HOME/SNP/SNP.pt > RESULTS/qc/ncm/vaf/T47D_BRCA1_Pg_7_20_23_L.BSB09421-1634.bwa-hg19.vaf`

Run on all the vaf files to get plot and summary file:

python $NCM_HOME/vaf_ncm.py -I RESULTS/qc/ncm/vaf -O RESULTS/qc/ncm -N NGSCheckMate