interval of the sort, merge, sampling and other functions

Content Transfer: https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.1.1/picard_util_IntervalListTools.php
GATK IntervalListTools combined in picard IntervalListToolsa plurality of operating features interval.

1. The combined two interval lists

java -jar picard.jar IntervalListTools \
      ACTION=CONCAT \
      I=input.interval_list \
      I=input_2.interval_list \
      O=new.interval_list

2. Merge two interval lists, and merge sort overlapping region

java -jar picard.jar IntervalListTools \
       ACTION=CONCAT \
       SORT=true \
       UNIQUE=true \
       I=input.interval_list \
       I=input_2.interval_list \
       O=new.interval_list 

3. Extract Another INPUT INPUT sequence from the

shell java -jar picard.jar IntervalListTools \ ACTION=SUBTRACT \ I=input.interval_list \ SI=input_2.interval_list \ O=new.interval_list ### 4.查找input1.interval_list或input2.interval_list,和在input3.interval_list中的碱基:shell
java -jar picard.jar IntervalListTools ACTION=INTERSECT I=input1.interval_list I=input2.interval_list SI=input3.interval_list O=new.interval_list
```

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Origin www.cnblogs.com/yuwq/p/11589479.html