User-defined coverage in CollectHsMetrics [Picard]
1
You can't, it's hard-coded: https://github.com/broadinstitute/picard/blob/master/src/main/java/picard/analysis/directed/TargetMetricsCollector.java#L692
metrics.PCT_TARGET_BASES_1X = ( double) targetBases[ 1] / ( double) targetBases[ 0] ;
metrics.PCT_TARGET_BASES_2X = ( double) targetBases[ 2] / ( double) targetBases[ 0] ;
metrics.PCT_TARGET_BASES_10X = ( double) targetBases[ 3] / ( double) targetBases[ 0] ;
metrics.PCT_TARGET_BASES_20X = ( double) targetBases[ 4] / ( double) targetBases[ 0] ;
metrics.PCT_TARGET_BASES_30X = ( double) targetBases[ 5] / ( double) targetBases[ 0] ;
metrics.PCT_TARGET_BASES_40X = ( double) targetBases[ 6] / ( double) targetBases[ 0] ;
metrics.PCT_TARGET_BASES_50X = ( double) targetBases[ 7] / ( double) targetBases[ 0] ;
metrics.PCT_TARGET_BASES_100X = ( double) targetBases[ 8] / ( double) targetBases[ 0] ;
alternatives:
change the code
use GATK DepthOfCoverage
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Yes, I saw it now.. I am doing it.
Thanks Pierre.
Hi, I'm bringing up an old post since I'm trying to obtain PCT target bases for 5x.
I'm not sure why we can't calculate it with the histogram values. What does the Histogram values represent?
The sum of all numbers in "high_quality_coverage_count" should be equal to "Total_reads" if we use Minimum_base_quality=0. Am I missing anything?