Question: how to set metrics file when using MarkDuplicates in Picard
0
gravatar for Yingzi Zhang
2.0 years ago by
Yingzi Zhang60
Jeddah
Yingzi Zhang60 wrote:

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

picard genome software error • 1.3k views
ADD COMMENTlink modified 2.0 years ago by zx87549.7k • written 2.0 years ago by Yingzi Zhang60
2
gravatar for Paul
2.0 years ago by
Paul1.4k
European Union
Paul1.4k wrote:

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.

ADD COMMENTlink written 2.0 years ago by Paul1.4k
1

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

ADD REPLYlink written 2.0 years ago by Yingzi Zhang60
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