Re: [Useq-users] Errors with VCF comparator

[David A. N. <dav...@gm...>]

Hello Ravi, 

I’ll take a look.  I suspect you don’t have any variants after filtering.  I’d first check if any variants are in your bed regions.  -cheers, D


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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