Picard CalculateHsMetrics perTargetCoverage for Novaseq bams

Picard CalculateHsMetrics perTargetCoverage for Novaseq bams

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Hello,
I would like to use Picard’s CalculateHsMetrics to calculate per target coverage for Novaseq bam files. It seems that the tool is not able to calculate mean/normalized coverage for Novaseq bams but works well with Hiseq bams. Novaseq bams report quality scores differently, therefore, my guess this is what is causing the issue. Do you have any suggestions.

java -jar /usr/local/bin/picard.jar CalculateHsMetrics 
BAIT_INTERVALS=targets.interval_list 
TARGET_INTERVALS=targets.interval_list 
INPUT=/alignT/test_clipped_overlaps.bam 
OUTPUT=/alignT/QC/test.HsMetrics.out 
REFERENCE_SEQUENCE=/ref/GRCh37/genome/human_g1k_v37.fasta 
PER_TARGET_COVERAGE=/alignT/QC/test.PerTargetCoverage.txt 
VALIDATION_STRINGENCY=SILENT 
METRIC_ACCUMULATION_LEVEL=ALL_READS 
VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false

Thanks


Picard

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