Picard CalculateHsMetrics perTargetCoverage for Novaseq bams
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
• 25 views
Read more here: Source link