CollectHsMetrics base coverage output has overlapping targets

Question

[blazer9131]

I am trying to get base coverage information, and am using the --PER_BASE_COVERAGE output to get a text file of base level coverage. However, some of my targets are being grouped together. In the targets file, these are separated by one base as such:

12      12258595        12258695        +       TARGET1
12      12258696        12258795        +       TARGET2
12      12258796        12259791        +       TARGET3

However, when I look at my covg file, I see the following:

chr    pos    target   covg 
12  12258595        TARGET1|TARGET2|TARGET3 510

Why would HSmetrics group these targets together, and how can I separate them?

[finswimmer]

Hello blazer9131 ,

• Which version of picard are you using?
• Could you please provide the full command line used?

Please tell us when you cross post your questions to other platforms. You also asked this question on stackexchange.

fin swimmer

[blazer9131]

Hi Fin,

I am using picard 2.17.11, here is what's being sent:

java -Xmx10g -jar picard_2.17.11.jar CollectHsMetrics I=${bam} O=${exp}.mq0.HSmetrics.txt BAIT_INTERVALS=$baits TARGET_INTERVALS=$targets REFERENCE_SEQUENCE=Homo_sapiens_assembly19.fasta PER_TARGET_COVERAGE=${exp}.mq0.target.covg TMP_DIR=/SCRATCH VALIDATION_STRINGENCY=LENIENT MINIMUM_MAPPING_QUALITY=0 MINIMUM_BASE_QUALITY=0 PER_BASE_COVERAGE=${exp}.mq0.base.covg