User: marta.rusmini

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Posts by marta.rusmini

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gene annotation with dbNSFP_gene
... Hi Other then annotate the variants in my vcf, I would also like to annotate the genes. In particular, I'm interested in a brief description of the gene in order to have a primary indication to prioritize and filter variants. I used dbNSFP for variants annotation but I cannot understand how to annta ...
gene next-gen written 12 months ago by marta.rusmini10 • updated 12 months ago by Kevin Blighe59k
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bcftools reheader -h
... Hi sorry for the very basic question! I would like to change the tags of the INFO fields of my vcf. I saw the bcftools -reader option but I cannot understand the format of the newheader.vcf that I need. Can anyone help me? I will appreciate help in order to a)create the new file needed for the scrip ...
header format bcftools written 15 months ago by marta.rusmini10 • updated 7 months ago by whitneyt0
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Comment: C: How to use snpSift annotate -info option to annotate specific fields of INFO
... 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: j`ava -jar path/to/SnpSift.jar dbnsfp -db /path/to//dbNSFP3.5a/dbNSFP3.5a.txt.gz \ –info ALLELEID,CLNDISDB \ prova.vcf > prova_dbNSFP-f.vcf` t ...
written 17 months ago by marta.rusmini10 • updated 17 months ago by finswimmer13k
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dbNSFP3.5a annotation. Error "Field name not found"
... Hi! I'm trying to annotate with dbNSFP3.5a (by using SnfSift) but I cannot solved an error. Can anyone help me? the error is " Error: Field name 'Uniprot_acc' not found" and the script I launched is java -jar /path/to/snpEff/SnpSift.jar dbnsfp -db /path/to/dbNSFP3.5a/dbNSFP3.5a.txt.gz \/myfile.vcf & ...
next-gen written 18 months ago by marta.rusmini10 • updated 17 months ago by Biostar ♦♦ 20

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