GC DROPOUT AND AT DROPOUT

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asqt96

• April 22, 2021 13:16

Hi, I ran your CollectGcBiasMetrics:

java -jar $PICARDPATH/picard_new.jar  CollectGcBiasMetrics \
      I=sample.bam \
      O=gc_bias_metrics.txt \
      CHART=gc_bias_metrics.pdf \
      S=summary_metrics.txt \
      R=reference

And I obtained this results:

ACCUMULATION_LEVEL      READS_USED      WINDOW_SIZE     TOTAL_CLUSTERS  ALIGNED_READS   AT_DROPOUT      GC_DROPOUT      GC_NC_0_19      GC_NC_20_39     GC_NC_40_59     GC_NC_60_79     GC_NC_80_100   SAMPLE  LIBRARY READ_GROUP
All Reads       ALL     100     4523644 9026596 5.563447        0.076132        1.321744        0.844959        0.990274        1.159031        0.879629

How do you interpret the AT_DROPOUT value? (5.563447) Which threshold do you suggest to use ?

Thank you in advance

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  Genevieve Brandt (she/her)

  • May 26, 2021 05:10

  This question I believe has been answered at the related thread here: https://gatk.broadinstitute.org/hc/en-us/community/posts/360077616251-GC-DROPOUT-DOUBT

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