Re: [Useq-users] How to use VCFComparator to compare two VCF files

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

Hello Gang,

Many thanks for the heads up.  Major bug here.  The filter for common regions was inadvertently disabled. Ugg!  I’ve posted an update to the Sourceforge site so download USeq_8.8.8 and disregard prior VCFComparator analysis.  Its not clear when this error occurred. Its easy to see if it hit your prior analysis, look at the number of test variants (or key variants) and make sure the pre and the post shared region numbers differ.

https://sourceforge.net/projects/useq/files/?source=navbar

I can’t seem to reproduce the SNP issue.  When I run without a -s or -n option both snp and indels are compared and written to the match and noMatch files.  Could you point me to your files and I’ll try to reproduce.

-cheers, David

On Nov 12, 2014, at 11:27 AM, Peng,Gang <GP...@md...> wrote:

> Dear all,
> 
> I am now using VCFComparator in USeq to compare two vcf files:
> 
> java -jar -Xmx10g ~/soft/USeq_8.8.5/Apps/VCFComparator 
> -a NISTIntegratedCalls_14datasets_131103_allcall_UGHapMerge_HetHomVarPASS_VQSRv2.18_all_nouncert_excludesimplerep_excludesegdups_excludedecoy_excludeRepSeqSTRs_noCNVs.vcf 
> 
> -b union13callableMQonlymerged_addcert_nouncert_excludesimplerep_excludesegdups_excludedecoy_excludeRepSeqSTRs_noCNVs_v2.18_2mindatasets_5minYesNoRatio.bed 
> 
> -c ../IonProton/IP.vcf 
> 
> -d ../IonProton/Ion-TargetSeq-b37_simp.bed
> 
>  -p ../IonProton/compare/
> 
> 
> According to the manual: "Only calls that fall in the common interrogated regions are compared.". But in the result:
> 
> 2195078292 Interrogated bps in key
> 47302058 Interrogated bps in test
> 33755093 Interrogated bps in common
> 2915731
> Key variants
> 2915731
> Key variants in shared regions
> 2.128631378 Shared key variants Ti/Tv
> 126539
> Test variants
> 126539
> Test variants in shared regions
> 2.050087979 Shared test variants Ti/Tv
> 
> And in the result vcf files, many positions are not in the shared bed file. It seems that all the variants in the two vcf files are compared. And by default, it should compare both SNPs and non SNPs. But in the result vcf files, there are only SNPs.
> 
> Do I need to change some parameters to compare the vcfs only in the interrogated regions and compare both SNPs and non-SNPs.
> 
> Thanks,
> Gang
> ------------------------------------------------------------------------------
> Comprehensive Server Monitoring with Site24x7.
> Monitor 10 servers for $9/Month.
> Get alerted through email, SMS, voice calls or mobile push notifications.
> Take corrective actions from your mobile device.
> http://pubads.g.doubleclick.net/gampad/clk?id=154624111&iu=/4140/ostg.clktrk_______________________________________________
> Useq-users mailing list
> Use...@li...
> https://lists.sourceforge.net/lists/listinfo/useq-users