How to use snpSift annotate -info option to annotate specific fields of INFO

Question

[MatthewP]

Hello, snpSift can annotate vcf file from other database vcf, and -info option to annotate specific fields.

You can use the -info command line option if you only want select only a subset of fields from db.vcf file.

I need some examples to show me how to use -info correctly.Example, my clinvar database vcf file:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
.....ALLELEID=446939;CLNDISDB=MedGen:C4015293,OMIM:616126,Orphanet:ORPHA319563;CLNDN=Immunodeficiency_38_with_basal_ganglia_calcification;..........ANN=A|missense_variant|MODERATE|ISG15|ISG15|transcript|NM......

If I don't want ANN fields because My vcf file already has, how do I do with -info?
If you don't have solutions for my case, but you did use -info before, It would be appreciate to show me your example command. Thanks.

Answer 1

[finswimmer]

Hello,

AFAIK there is no option in snpSift to say "take all info fields but ...". You can take all fields from the info column by applying -info or add a comma separated list of filed names to the -info parameter, e.g. -info ALLELEID,CLNDISDB.

You could also use -name <prefix> to prepend a prefix to each info field. Doing this you can avoid duplicate fields.

fin swimmer

[marta.rusmini]

Hi! can you help me in order to understand an error regarding this -info option? I'm trying to use the -f option but it seems not working. my script: java -jar path/to/SnpSift.jar dbnsfp -db /path/to//dbNSFP3.5a/dbNSFP3.5a.txt.gz \ –info ALLELEID,CLNDISDB \ prova.vcf > prova_dbNSFP-f.vcf

the error: Error: Unknown extra parameter 'ALLELEID,CLNDISDB' SnpSift DbNsfp SnpSift version 4.3p (build 2017-06-06 09:55), by Pablo Cingolani

I tried to use different columns but the error is always the same.

Thank you in advance

[finswimmer]

According to the manual you have to use the -fparameter to define the fields, when using dbnsfp:

You can now specify which fields you want to use for annotation using the '-f' command line option followed by a comma separated list of field names. Defaults fields are shown when running the command without any arguments java -jar SnpSift.jar dbNSFP.

fin swimmer

[MatthewP]

Hello, did you missing "annotate" param? My command like

java -jar /software/snpEff/SnpSift.jar annotate -info ALLELEID,CLNDN database.gz sample.vcf > result.vcf

this works.