Vcf-annotate does not work

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Ilya Ogurtsov

• January 25, 2020 22:30

Hello, colleagues!

Could you, please, help or give a hint what's wrong?

My HaplotypeCaller and VariantFiltration tools are Version=3.4-46-gbc02625

Java used is: jre1.8.0_231

I use the following command:

cat our.vcf | vcf-annotate -a home/dbSNP/All_20180418.vcf.gz -d key=INFO,ID=ANN,Number=1,Type=Integer,Description='dbSNP' -c CHROM,POS,ID,REF,ALT,-,-,- > our.dbSNP.vcf

I have no log after calling the command (maybe I do not know where the log is written). Command line returns in few seconds (obviously nothing is done through these moments) with exact vcf file which i gave to the command as input.

I use All_20180418.vcf.gz with index file All_20180418.vcf.gz.tbi from National Library of Medicine (ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/VCF/) in the same folder.

The titles of my input vcf file and the brief content is below:

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT OncoUnite

chr1 113249 . AC A 38.70 PASS AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=19.35;SOR=2.303 GT:AD:DP:GQ:PL 1/1:0,2:2:6:75,6,0

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  Tiffany Miller

  • January 27, 2020 18:44

  Hello Ilya Ogurtsov - sorry, vcf-annotate is not a part of the GATK so I am not sure what could be going on here. If anyone else in the community has used it and wants to comment, go for it!

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