how to set metrics file when using MarkDuplicates in Picard
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4.1 years ago
Yingzi Zhang ▴ 70

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

software error genome picard • 2.3k views
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4.1 years ago
Paul ★ 1.5k

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.

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