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Coverage ATAV Command

CCDS real-estate coverage summary and comparison to controls:

atav.sh --coverage-comparison --sample <sample file> --gene-boundaries /nfs/goldstein/goldsteinlab/Bioinformatics/scripts/CCDS_public_releases/addjusted.CCDS.genes.index.r14.txt --min-coverage 10 --out <desired output file location>

Refer to output file with suffix "sample.summary.csv" for the information about what percentage of the CCDS (release 14) was covered with at least 10-fold coverage in each sample.