If I was going to view a bam file in IGV both with duplicayes marked and then after they are removed are these commands accurate:
Flag duplicates in BAM
Remove duplicates from BAM
Are there additional options to use?
Thank you .
Flag duplicates in BAM
Code:
java -jar picard.jar MarkDuplicates \ INPUT=sorted_reads.bam \ OUTPUT=dedup_reads.bam \ METRICS_FILE=metrics.txt
Code:
java -jar picard.jar MarkDuplicates \ INPUT=sorted_reads.bam \ OUTPUT=dedup_reads.bam \ REMOVE_DUPLICATES=true \ METRICS_FILE=metrics.txt
Thank you .