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