Germline CNV for WES data:FilterIntervals/ GermlineCNVCaller error

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Heba B abusamra

• August 06, 2020 20:55

(REQUIRED) For us to most effectively understand your question, please fill in your responses below:

a) I am using GATK version (v.4.1.8.1)
b) The specific command(s) I used is/are

gatk PreprocessIntervals -L NexteraRapidCapture_Exome_Probes_v1.2.bed -R ../Genome/genome.fa -O target.preprocessed.interval_list -imr OVERLAPPING_ONLY --bin-length 0 --padding 250

gatk CollectReadCounts -I PBG-1095-19_S2.bam -L target.preprocessed.interval_list --interval-merging-rule OVERLAPPING_ONLY --format TSV -O PBG-1095-19_S2.tsv

/gatk CollectReadCounts -I PBG-1077-19R_S8.bam -L target.preprocessed.interval_list --interval-merging-rule OVERLAPPING_ONLY --format TSV -O PBG-1077-19R_S8.tsv

gatk CollectReadCounts -I PBG-1076-19R_S7.bam -L target.preprocessed.interval_list --interval-merging-rule OVERLAPPING_ONLY --format TSV -O PBG-1076-19R_S7.tsv

gatk CollectReadCounts -I PBG-1096-19_S1.bam -L target.preprocessed.interval_list --interval-merging-rule OVERLAPPING_ONLY --format TSV -O PBG-1096-19_S1.tsv

==========================================================================================================
gatk AnnotateIntervals -L nextera_dna_exome_targeted_regions_manifest_v1_2.bed -R ../Genome/genome.fa -O target.preprocessed.annotated.tsv -imr OVERLAPPING_ONLY

gatk FilterIntervals -L nextera_dna_exome_targeted_regions_manifest_v1_2.bed --annotated-intervals target.preprocessed.annotated.tsv -I PBG-1095-19_S2.tsv -I PBG-1077-19R_S8.tsv -I PBG-1076-19R_S7.tsv -I PBG-1096-19_S1.tsv -imr OVERLAPPING_ONLY -O target.gc.filtered.interval_list

c) Please post error log here

when run the filterintervals command it gave an error

23:23:16.268 INFO IntervalArgumentCollection - Processing 45326818 bp from intervals
23:23:16.560 INFO FilterIntervals - Shutting down engine
[August 6, 2020 11:23:16 PM AST] org.broadinstitute.hellbender.tools.copynumber.FilterIntervals done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=751828992
java.lang.IllegalArgumentException: At least one interval must remain after intersection.
at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:725)
at org.broadinstitute.hellbender.tools.copynumber.FilterIntervals.resolveAndValidateIntervals(FilterIntervals.java:341)


when I tried to proceed and run cohort mode of 

gatk DetermineGermlineContigPloidy -L target.preprocessed.interval_list --interval-merging-rule OVERLAPPING_ONLY -I PBG-1095-19_S2.tsv -I PBG-1077-19R_S8.tsv -I PBG-1076-19R_S7.tsv -I PBG-1096-19_S1.tsv --contig-ploidy-priors contig_ploidy_priors.tsv --output . --output-prefix ploidy --verbosity DEBUG--> ran fine

gatk GermlineCNVCaller --run-mode COHORT -L target.preprocessed.interval_list -I PBG-1095-19_S2.tsv -I PBG-1077-19R_S8.tsv -I PBG-1076-19R_S7.tsv -I PBG-1096-19_S1.tsv --contig-ploidy-calls ploidy-calls \
--annotated-intervals target.preprocessed.annotated.tsv \
--interval-merging-rule OVERLAPPING_ONLY \
--output cohortPon \
--output-prefix cohortPon --verbosity DEBUG --> gave an error

java.lang.IllegalArgumentException: Annotated intervals do not contain all specified intervals.
at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:725)
at org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberArgumentValidationUtils.validateAnnotatedIntervalsSubset(CopyNumberArgumentValidationUtils.java:165)

 

How I can solve these errors.

I m trying to build the CNV pipeline script for CNV detection using gcnv on case mode and as i understand the steps are briefly as 

1. PreprocessIntervals 

2. Collect Read Counts

3. AnnotateIntervals / filterintervals

4. DetermineGermlineContigPloidy ( in cohort mode to build cohort model)

5. GermlineCNVCaller --run-mode COHORT

6. DetermineGermlineContigPloidy ( build case calls)

7. GermlineCNVCaller --run-mode case

8. PostprocessGermlineCNVCalls

is it correct?

0

• 

  Genevieve Brandt (she/her)

  • August 07, 2020 15:58

  There are issues with how you are using your intervals, check the interval files before and after each command to make sure that the output is how you expect.

  See here for more explanation: 

  • https://gatk.broadinstitute.org/hc/en-us/articles/360035531152--How-to-Call-common-and-rare-germline-copy-number-variants
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  Troy LoBue

  • April 06, 2021 17:26

  I received the same error output for the FilterIntervals command and can not find a solution. 

   

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  Genevieve Brandt (she/her)

  • April 07, 2021 15:27

  Heba B abusamra were you able to find a solution to this issue?

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  Genevieve Brandt (she/her)

  • April 16, 2021 19:46

  Hi Troy LoBue, if you are still working with this issue, here is the information we need to look into GATK issues: https://gatk.broadinstitute.org/hc/en-us/articles/360053845952-Forum-Guidelines#write_a_new_post

  Genevieve

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