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!?
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Jimbou
1 answer
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.
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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.