BedToIntervalList Error

Follow

Vincent Appiah

• September 03, 2020 13:48

Hello Team, I am running gatk  4.1.1.0 BedToIntervalList command on my bedfile. The interval list will be used to create a panel of normals for  variant calling on my whole exome sequence I tried with both hg38 and hg19 but they all give me the same error below

picard.PicardException: Start on sequence 'chr1' was past the end: 248956422 < 249104618
at picard.util.BedToIntervalList.doWork(BedToIntervalList.java:148)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:295)
at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:25)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
at org.broadinstitute.hellbender.Main.main(Main.java:291)

 

I used the command below

gatk BedToIntervalList \
-I $bedfile \
-O list.interval_list \
-SD $dict \
--VALIDATION_STRINGENCY SILENT

Please advice

0

• 

  David Benjamin

  • September 03, 2020 18:00

  Vincent Appiah $dict and $bedFile are probably inconsistent.  It looks like your BED file contains an interval on chr1 that starts at 249104618, while your sequence dictionary says chr1 ends at 248956422, which is the case for hg38.  In hg19 chr1's length is 249250621 and you should have no problems.

  0

  Comment actions Permalink
• 

  Vincent Appiah

  • September 03, 2020 20:41

  Hi David,

  You are right. I was able to run using hg19. Thanks for the info

  0

  Comment actions Permalink

Please sign in to leave a comment.