Funcotator log says "Cannot create complete funcotation for variant at chr1:25813992-25814012 due to alternate allele: *"
REQUIRED for all errors and issues:
a) GATK version used:gatk-4.4.0.0
b) Exact command used:gatk Funcotator \
--variant /public/slst/home/lict/ZYJ/sladuk/gatk/filtered.I8_L1.rdup.SNC.RG.vcf \
--reference /public/slst/home/lict/ZYJ/referenceseq/GRCh38.p14.genome.fa \
--ref-version hg38 \
--data-sources-path /public/slst/home/lict/ZYJ/referenceseq/funcotator/funcotator_dataSources.v1.7.20200521s/ \
--output ./filtered.I8_L1.rdup.SNC.RG.funcotated.vcf \
--output-file-format VCF
c) Entire program log:
part of log looks like this, I generated my vcf with RNAseq short variant discovery (SNPs + Indels) . And in my annotated maf all snps not in database discovered are not shown. I don't know why this is happening and is it related to the warning in log file.
Thanks!
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Hi 周尤佳
Seems like an edge case has occurred therefore Funcotator could not solve it. Can you try with a nightly build of GATK from docker (or you can build one yourself from the master branch) with resource bundle 1.8 for Funcotator to see if this problem persists?
Regards
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Hi Gökalp,
Thanks for the help, I also want to know if Funcotator is designed to output snps presenting in the database only, because I found all my snps not in the database are filtered out or just not annotated.
I would like to know about these undocumented mutations because I kind of induced mutations and tried to detect them.
Thanks!
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Hi again.
Funcotator is not limited to a certain set of variants but can work all major short variants that are included within the resource bundle transcripts and genome build. If you think that even the latest build of Funcotator and GATK resource bundle does not solve your problem you may try using alternative annotators such as Variant Effect Predictor from ensembl to see if they work for your case.
I hope this helps.
Regards.
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