Using Picard "CalculateHsMetrics" to find coverage stat

[serenaliao]

Hi all,

I have been trying to use CalculateHsMetrics to get coverage information. I have two questions:

1. When I run the code:
java -Xmx10g -jar /home/liao/picard-tools-1.96/CalculateHsMetrics.jar BAIT_INTERVALS=target.bed TARGET_INTERVALS=target.bed INPUT=/data2/Pregnent_1_time_6_month/SAM/V8_GCCAAT_L003_R1_001.fastq.gz_bismark_pe.sam OUTPUT=sample.hybrid.stats.txt
Everything went well, and it took 20 mins to finish. However after I added PER_TARGET_COVERAGE options, and reference genome(fa extension), after a few seconds there's nothing, and no longer runnning:
java -Xmx10g -jar /home/liao/picard-tools-1.96/CalculateHsMetrics.jar BAIT_INTERVALS=target.bed TARGET_INTERVALS=target.bed INPUT=/data2/Pregnent_1_time_6_month/SAM/V8_GCCAAT_L003_R1_001.fastq.gz_bismark_pe.sam OUTPUT=sample.hybrid.stats.txt PER_TARGET_COVERAGE=Picard_PER_TARGET_COVERAGE.txt R=/home/liao/mm9/genome.fa
Does anyone know how to solve it?

2. So the near bait reads(according to their code) use 250 +/- off baits regions as criteria. Is there any convenient way to adjust the number, say to 10K,20K...?


Thanks in advance!!