Re: [Useq-users] Errors with VCF comparator

[David N. <Dav...@hc...>]

Hello Ravi,

Looks like the issue is with missing/ no vcf records after filtering causing the app to abort.  I’ve put in a bunch of catches for this.  Give USeq_8.7.7 a try https://sourceforge.net/projects/useq/  It’s just going to abort with what I hope is an informative error message instead of the stack trace.

Note for future reference, I’m hamstrung trying to debug using dummy datasets, see if you can post the real ones of interest next time.  http://bioserver.hci.utah.edu/BioInfo/index.php/FAQ#How_do_I_report_a_problem_or_issue_with_a_USeq_application.3F

-cheers, D

-- 
David Austin Nix, PhD
Huntsman Cancer Institute
Dept. OncSci University of Utah
Bioinformatics Shared Resource
HCI 3165 (801) 587-4611
dav...@hc...

On Mar 3, 2014, at 4:35 PM, Ravi Vijaya Satya - QIAGEN <Rav...@qi...> wrote:

> I am using VCFComparator from the USeq_8.7.6 package. This tool very useful in comparing with NIST GIB calls. However, there seems to be a bug in the code that is triggered by some bed files while others work fine. 
> 
> Exception in thread "main" java.lang.NegativeArraySizeException
>        at edu.utah.seq.vcf.VCFParser.filterVCFRecords(VCFParser.java:325)
>        at edu.utah.seq.vcf.VCFComparator.parseFilterFiles(VCFComparator.java:420)
>        at edu.utah.seq.vcf.VCFComparator.<init>(VCFComparator.java:69)
>        at edu.utah.seq.vcf.VCFComparator.main(VCFComparator.java:515)
> 
> 
> In an effort to narrow the problem down, I supplied a VCF with no variant calls (but a header), and still got the error with  this bed file. I am comparing against NIST 2.18 calls. My command line:
> 
> 
> java -jar -Xmx22g /mnt/fdkbio05/rvijaya/software/USeq_8.7.6/Apps/VCFComparator -a ~/misc/NA12878_NIST/NISTIntegratedCalls_14datasets_131103_allcall_UGHapMerge_HetHomVarPASS_VQSRv2.18_all_nouncert_excludesimplerep_excludesegdups_excludedecoy_excludeRepSeqSTRs_noCNVs.vcf -b ~/misc/NA12878_NIST/union13callableMQonlymerged_addcert_nouncert_excludesimplerep_excludesegdups_excludedecoy_excludeRepSeqSTRs_noCNVs_v2.18_2mindatasets_5minYesNoRatio.bed -c dummy.vcf -d test.bed -p NIST_comparison
> 
> Any pointers on fixing this problem? I am attaching the vcf and the bed files that I am using. 
> 
> Thanks,
> Ravi<test.bed><dummy.vcf>------------------------------------------------------------------------------
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