Looking for picard per_target_coverage output field definitions

lracacholracacho OttawaMember

Hello, I ran Picard CollectHSmetrics with the optional per_target_coverage output and I am looking for the definitions of the following fields: "%GC", "mean_coverage", "normalized_coverage" (the definition for this field was already posted), "min_normalized coverage", "max_normalized coverage", "min_coverage", "max_coverage", "pct_0x" and "read_count".


Best Answer


  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    HI @lracacho

    Here is a link to the document with the metrics definitions you are looking for: https://broadinstitute.github.io/picard/picard-metric-definitions.html

  • lracacholracacho OttawaMember

    Thank you for the quick reply!

    I have previously looked at the picard-metric-definitions but I could not find the field definitions specifically for the "per_target_coverage" output. In addition to regular HSmetrics, per_target_coverage and per_base_coverage are output options.

    I was able to locate a similar field to "pct_0x". Under the heading for tool TargetedPcrMetrics, ZERO_CVG_TARGETS_PCT is defined as "The fraction of targets that did not reach coverage=1 over any base." Is this the same definition used for the per_target_coverage field "pct_0x"?


  • lracacholracacho OttawaMember

    Thank you! I have one more question....What is the relationship between max_coverage and read_count? For example, for one target region I have a read count of 192 and a min_coverage of 12 and a max_coverage of 32. This field read_count can't be the average across the target region.

  • AdelaideRAdelaideR Unconfirmed, Member, Broadie, Moderator admin

    The coverage is relevant to the "active region" as defined by the HaplotypeCaller.

    MAX_TARGET_COVERAGE The maximum coverage of reads that mapped to target regions of an experiment. This can be affected by two other parameters, MINIMUM_MAPPING_QUALITY (default=20) and MINIMUM_BASE_QUALITY (default=20). So reads with a low mapping quality and bases with a low quality are not considered for the target coverage calculations. Is your mapping quality lower for some samples in this region?

    Take a look at this conversation to see if that answers the question.

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