how to set metrics file when using MarkDuplicates in Picard

Question

[Yingzi Zhang]

Dear all,

I tried to use Picard MarkDuplicates to mark duplicates. I found METRICS_FILE need to be set. However, I know nothing about the "metrics"about my data. All I know is its mapping rate, etc. What should I look into and how should I set the matrics file please? Thank you.

Yingzi

Answer 1

[Paul]

Hi, my syntax looks like:

picard -Xmx"$memory"g -Djava.io.tmpdir=$PWD/tmp -XX:ParallelGCThreads=$cpu MarkDuplicates I= ${p%.bam}.bam O= ${p%.bam}_rmdp.bam METRICS_FILE= ${p%.bam}_rmdp.txt CREATE_INDEX=true USE_JDK_DEFLATER=true USE_JDK_INFLATER=true

Metrics should give you an statistics about PCR duplicates.

[Yingzi Zhang]

Yes. I found that the Matrics is not an input file but an output file. Thank you!