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

[Peng,Gang <GP...@md...>]

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