User: sara_wasl

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sara_wasl0
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Posts by sara_wasl

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Comment: C: Mutation count in multi-sample vcf file
... Sorry but that what I understand from your post above with: $ curl -s -k "https://raw.github.com/arq5x/gemini/master/test/test4.vep.snpeff.vcf" |\ java -jar dist/groupbygene.jar ...
written 2 days ago by sara_wasl0
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Comment: C: Mutation count in multi-sample vcf file
... This is more logical, I'm thinking that the command you provided not correct: file.vcf |\ java -jar dist/groupbygene.jar This is what I have been tried and give me the error. ...
written 3 days ago by sara_wasl0
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Comment: C: Mutation count in multi-sample vcf file
... See here: https://gist.github.com/SaraAlthubaiti/6b52f727165e707add3a99c4414e91ac ...
written 3 days ago by sara_wasl0
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Comment: C: Mutation count in multi-sample vcf file
... The input file was the one after annotated using SnpEff, This is what I got for **grep -m1 CHROM myfile.ann.vcf** : #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT LIBRARY_NAME=S2000 2:LIBRARY_NAME=S2000 3:LIBRARY_NAME=S2000 4:LIBRARY_NAME=S2000 5:LIBRARY_NAME=S2000 6:LIBRARY_NAME=S2000 7:LIBRARY ...
written 4 days ago by sara_wasl0
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Comment: C: Mutation count in multi-sample vcf file
... Thanks for the help, I try to run **GroupByGene** using the same command and file just to see the output but it gives this error. Also when I tried my file (I was concerning if the problem from my file but that also happen for the provided file): [SEVERE][GroupByGene]Your input file has a malfo ...
written 4 days ago by sara_wasl0
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Comment: C: Mutation count in multi-sample vcf file
... After annotating with SnpEff and running GroupByGene, I got this error: [SEVERE][GroupByGene]Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file htsjdk.tribble.TribbleException$InvalidHeader: Your input file has a ...
written 4 days ago by sara_wasl0
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Comment: C: Mutation count in multi-sample vcf file
... Could you please help me with the annotation, I'm new to that field. Are there clear steps for the annotation? ...
written 5 days ago by sara_wasl0
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Comment: C: Mutation count in multi-sample vcf file
... Just to make sure, here `"https://raw.github.com/arq5x/gemini/master/test/test4.vep.snpeff.vcf"` it should be my vcf file **after** annotated by VEP or SnpEff, right? ...
written 5 days ago by sara_wasl0
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Mutation count in multi-sample vcf file
... Hello all, I have a one vcf file of 26 samples, what I need is to annotate this file and count the number of mutations for each gene for each sample of those 26. I tried to use Annovar, but it seems that it doesn't support multi-sample vcf file. Any suggestion or help, please? ...
vcf annotate mutations count written 5 days ago by sara_wasl0 • updated 5 days ago by Pierre Lindenbaum112k
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Comment: C: Download STRING database with Protein name
... Thanks a lot now it's work well with me, the problem was from the type of the data not from the server. But I notice that a lot of the Ensembl protein were ignored, so, for example, I enter around 11 million Ensembl protein and I got after conversion around 39 thousand!! ...
written 7 days ago by sara_wasl0

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