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vctrymao

• April 22, 2020 01:25

Using GATK 4.1.2.0. 

I am getting the following error: 

```

A USER ERROR has occurred: File /path/to/0049-scattered.interval_list is malformed: Interval file could not be parsed in any supported format. caused by Couldn't read file file:///path/to/0049-scattered.interval_list. Error was: file:///path/to/0049-scattered.interval_list has an invalid interval : hs37d5:1-35477943   +       .

```

I use the Broad b37 reference (ie. Homo_sapiens_assembly19.fasta). I created this interval list using GATK's SplitIntervals script so I'm not sure why it would error out like this. Do you know why? 

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• 

  Bhanu Gandham

  • April 22, 2020 19:02

  HI vctrymao

   

  Take a look at this doc: https://gatk.broadinstitute.org/hc/en-us/articles/360035531852-Intervals-and-interval-lists

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