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
.