Question: How to use snpSift annotate -info option to annotate specific fields of INFO
0
gravatar for MatthewP
10 months ago by
MatthewP260
China
MatthewP260 wrote:

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.

annotation snpsift • 752 views
ADD COMMENTlink modified 10 months ago by finswimmer12k • written 10 months ago by MatthewP260
3
gravatar for finswimmer
10 months ago by
finswimmer12k
Germany
finswimmer12k wrote:

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

ADD COMMENTlink written 10 months ago by finswimmer12k

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

ADD REPLYlink modified 10 months ago by finswimmer12k • written 10 months ago by marta.rusmini0

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

ADD REPLYlink written 10 months ago by finswimmer12k

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.

ADD REPLYlink written 10 months ago by MatthewP260
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