Re: [Useq-users] Errors with VCF comparator

[Ravi V. S. - Q. <Rav...@qi...>]

Hi David,

Thanks for looking into this. If there are no GIB variants in my Bed regions, then all my calls should be reported as false positives, right? There might be individual bed intervals without GIB variants, but there are certainly some GIB variants in all my bed intervals put together. 

Thanks,
Ravi

-----Original Message-----
From: David Austin Nix [mailto:dav...@gm...] 
Sent: Tuesday, March 04, 2014 11:17 AM
To: Ravi Vijaya Satya - QIAGEN
Cc: USeq
Subject: Re: [Useq-users] Errors with VCF comparator

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_UGHa
> pMerge_HetHomVarPASS_VQSRv2.18_all_nouncert_excludesimplerep_excludese
> gdups_excludedecoy_excludeRepSeqSTRs_noCNVs.vcf -b 
> ~/misc/NA12878_NIST/union13callableMQonlymerged_addcert_nouncert_exclu
> desimplerep_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>---------------------------------------------
> --------------------------------- Subversion Kills Productivity. Get 
> off Subversion & Make the Move to Perforce.
> With Perforce, you get hassle-free workflows. Merge that actually works. 
> Faster operations. Version large binaries.  Built-in WAN optimization 
> and the freedom to use Git, Perforce or both. Make the move to Perforce.
> http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.
> clktrk_______________________________________________
> Useq-users mailing list
> Use...@li...
> https://lists.sourceforge.net/lists/listinfo/useq-users