Fig. 1: Summary of the VCPA-WES pipeline.
From: Human whole-exome genotype data for Alzheimer’s disease
Components with “stars” are modified upon VCPA-WGS pipeline. VCPA-WES specific scripts included: CRAM metrics generation (stage1/wes_depthOfCoverage.sh), gVCF metrics generation (stage2b/wes_no_target_hc_full_bam.sh, stage2b/wes_variantEval.sh), VQSR model generation (stage 3/VQSR_snp_WES.sh, stage 3/VQSR_indel_WES.sh, stage 3/ApplyRecalibration_GATK411_SNP_WES.sh,stage3/ApplyRecalibration_GATK411_indel_WES.sh). All these can be found at https://bitbucket.org/NIAGADS/vcpa-pipeline/src/master/VCPA/.
