Allelic CNV (common snps and getbayesianhetcoverage

I created a list of common SNPs for GetBayesianHetCoverage following https://gatkforums.broadinstitute.org/gatk/discussion/7812/creating-a-list-of-common-snps-for-use-with-getbayesianhetcoverage.
I used GATK 3.7 (because no "CatVariants" in GATK 4?) with
Hg19 fasta (from ftp://ftp.ncbi.nlm.nih.gov/sra/reports/Assembly/GRCh37-HG19_Broad_variant/).
and got allchr.1kg.phase3.v5a.snp.maf10.biallelic.hg19.interval_list.

When I ran "GetBayesianHetCoverage (gatk-4.beta.6)", I got the following error:

04:38:01.403 INFO GetBayesianHetCoverage - Shutting down engine
[November 29, 2017 4:38:01 AM CST] org.broadinstitute.hellbender.tools.exome.GetBayesianHetCoverage done. Elapsed time: 0.21 minutes.
Runtime.totalMemory()=5701107712
htsjdk.samtools.SAMException: Intervals not in order: 9:141146683-141146683 + rs374057746; 10:60969-60969 + rs61838556
at htsjdk.samtools.util.IntervalUtil.assertOrderedNonOverlapping(IntervalUtil.java:70)
at htsjdk.samtools.filter.IntervalFilter.(IntervalFilter.java:57)
at htsjdk.samtools.util.SamRecordIntervalIteratorFactory.makeSamRecordIntervalIterator(SamRecordIntervalIteratorFactory.java:67)
at htsjdk.samtools.util.AbstractLocusIterator.iterator(AbstractLocusIterator.java:192)
at org.broadinstitute.hellbender.tools.exome.pulldown.BayesianHetPulldownCalculator.getHetPulldown(BayesianHetPulldownCalculator.java:339)
at org.broadinstitute.hellbender.tools.exome.GetBayesianHetCoverage.runMatchedNormalTumor(GetBayesianHetCoverage.java:344)
at org.broadinstitute.hellbender.tools.exome.GetBayesianHetCoverage.doWork(GetBayesianHetCoverage.java:385)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:119)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:176)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:195)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:131)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:152)
at org.broadinstitute.hellbender.Main.main(Main.java:233)

(Command line:
java -jar gatk-package-4.beta.5-local.jar GetBayesianHetCoverage \
--reference genome.fa \
--snpIntervals allchr.1kg.phase3.v5a.snp.maf10.biallelic.hg19.interval_list \
--tumor tumor.bam \
--tumorHets tumor_het_pulldown.tsv \
--normal normal.bam \
--normalHets normal_het_pulldown.tsv \
--hetCallingStringency 30)

I also tried picard "GatherVcfs" (replace CatVariants) and "SortVcf"(for interval order), but it was no use.
Please teach me how to solve it .
Thank you.

Answers

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