SnpSift Annotate replace ID column

Question

[Jimbou]

Is it possible to use SnpSift Annotate function to replace values already existing in the ID column?

java -jar SnpSift.jar annotate -id 00-common_all.vcf.gz my_sample.vcf 

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT
22      16050435        22:16050435     T       C       .       PASS    AF=0.00029;MAF=0.00029;R2=0.00226       GT:DS:GP
22      16050783        22:16050783;rs587743568 A       G       .       PASS    AF=0.00023;MAF=0.00023;R2=0.00015;ASP;CAF=0.9922,0.007788;COMMON=1;KGPhase3;RS=587743568;RSPOS=16050783;SAO=0;SSR=0;VC=SNV;VP=0x050000000005000026000100;WGT=1;dbSNPBuildID=142    GT:DS:GP
22      16050822        22:16050822     G       A       .       PASS    AF=0.14691;MAF=0.14691;R2=0.05570       GT:DS:GP

But unfortunatly using the SNP files from here ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/VCF/ will add rsIDs only in a semicolon separated fashion. See line three for instance: 22:16050783;rs587743568

A further side effect is that the parameters -id or -info are not working. In both cases all information is added like when no parameter is specified. Perhaps the dbSnp files 151 are corrupt/not compatible with the recent release of SnpSift!?

[Nicholas Mancuso]

I'm running into this exact problem right now. SnpSift seems like the only tool that is smart with respect to ALT/REF ordering and having it replace existing IDs would be a huge boon.

Answer 1

[Nicholas Mancuso]

I'm not sure that the original SnpSift can do it. However, I forked SnpSift and hacked the code to always replace if the ID is found in the annotation file. You can find the new code here: https://github.com/quattro/SnpSift

It does need to be rebuilt using maven following the instructions on the main SnpEff site to work.