FAQ

Waltz Metrics Files

• .covered-regions

  • chr

  • start

  • end

  • length

  • average coverage in the contiguous region

  • total coverage in the contiguous region

• .read-counts

  • bam file name

  • total reads

  • unmapped reads

  • total mapped reads

  • unique mapped reads

  • duplicate fraction

  • total on-target reads

  • unique on-target reads

  • total on-target rate

  • unique on-target rate

• .fragment-sizes

  • fragment-size

  • total frequency

  • unique frequency

• -pileup-without-duplicates.txt

  • similar to above but only unique fragments are counted

• -intervals.txt Header

  • chr

  • start

  • end

  • interval name

  • interval length

  • peak coverage

  • average coverage

  • GC fraction

  • number of fragments mapped

• -intervals-without-duplicates.txt

  • similar to above but only unique fragments are considered

After aggregate_bam_metrics.sh (aggregate across samples):

• waltz-coverage.txt - per sample coverage calculated across chosen genomic intervals

• fragment-sizes.txt - fragment size distributions for all samples