Picard Metrics

Hi all,
I have 2 questions about the Picard metrics.
Sorry if they are stupid or you have already answered but I didn't find anything googling or searching in this forum.
1. HsMetrics: in the page of metrics definition it is declared that the tool returns the percentage of all target bases achieving 2x,10x,20x,30,40x,50x,100x but when I run the command in the output file there are only 2x,10x,20x,30x.
Is that correct? Is there any option I have to use to add information about 40x,50x and 100x?
My command is:

java -jar CalculateHsMetrics.jar \
BAIT_INTERVALS=PICARD_interval_list_CANCER.list \
REFERENCE_SEQUENCE=hg19.fa \
TARGET_INTERVALS=PICARD_interval_list_CANCER.list \
BAIT_SET_NAME=CANCER \
METRIC_ACCUMULATION_LEVEL=SAMPLE \
INPUT=sample.bam\
OUTPUT=sample.metrics

  1. In the PICARD metric page I found metrics about VariantCalling:
    https://broadinstitute.github.io/picard/picard-metric-definitions.html#CollectVariantCallingMetrics.VariantCallingDetailMetrics
    But I didn't find the associated Picard tool. Is that an old metric not in use anymore?

Thanks for the help, hope to not bother you.

java -jar CalculateHsMetrics.jar --version
1.66(1178)
Linux version 2.6.32-279.2.1.el6.x86_64 ([email protected])

Tagged:

Issue · Github
by Sheila

Issue Number
135
State
closed
Last Updated
Closed By
chandrans

Best Answer

Answers

  • deklingdekling Broad InstituteMember admin

    Sounds like low coverage. However, if you send us the output file, we can have a better idea of what is happening. Thanks, -David

  • KurtKurt Member ✭✭✭

    Your picard version is very, very old so they might not have come out until later (for your #1 question).

    For #2, same thing, CollectVariantCallingMetrics is pretty new.

    CollectVariantCallingMetrics is in version 1.138 but not in version 1.126 (those are the two I just check).

    Also, be aware that newer version of picard have a different command line invocation. For example, with your version, you invoke CalculateHSmetrics by;

    java -jar CalculateHSmetrics.jar

    For newer versions (after version 1.119) it is invoked by;

    java -jar picard.jar CalculateHSmetrics

  • merella.stefaniamerella.stefania ItalyMember

    Thanks for the answers!!

    @dekling I attached an example file, but I doubt that it is a problem of coverage.. as mean coverage I have 252.8397 ...

    @Kurt I will update my PICARD version and I will let you know if it works.
    After the update, for the CollectVariantCallingMetrics which tool I have to call?

    Thanks a lot for the help!!

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