User: A

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Posts by A

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Should I keep up with random contigs in human genome
... Hi I have a big annovar annotation of my SNV and INDEL from whole genome sequencing In chromosome column I have chr 1 to 22 and another contigs like > unique(anno_maf$Chromosome) [1] "chr1" "chr6" [3] "chr16" "chr17" ...
vcf wgs somatic variation written 3 days ago by A3.7k • updated 2 days ago by WouterDeCoster42k
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Some clarification on Strelka output
... Hi In this link https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md#somatic The somatic allele frequency estimate in the tumor sample is not directly available in the VCF output But I am seeing somatic allele frequency here in Strelka vcf for SNVs chrM 1097 . G A . ...
vcf strelka vaf wgs written 7 days ago by A3.7k
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Comment: C: Is this range of VAF is ordinary?
... Sorry @ATpoint, I googled but I failed to find a full documentation explaining what each part of a vcf from Strelka means especially INFO column. Please can you share if you found such documentation? ...
written 11 days ago by A3.7k
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Comment: C: Is this range of VAF is ordinary?
... Not at all. You are very welcome to comment ...
written 13 days ago by A3.7k
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Comment: C: Is this range of VAF is ordinary?
... Sorry in my 5 years membership in biostars I realised that most of times you used to commenting on OP's posts in a harsher way than the other mediators used to. I admit that I am too bad in deep and logical thinking but I don't think this would justify the way you are commenting. By mentioning "HE", ...
written 13 days ago by A3.7k
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Comment: C: Is this range of VAF is ordinary?
... For INDELs he has written #Basic information chrom=$(echo $line | sed 's/ /\t/g' | cut -f 1) #&& echo $chrom; Pos=$(echo $line | sed 's/ /\t/g' | cut -f 2) #&& echo $Pos; Ref=$(echo $line | sed 's/ /\t/g' | cut -f 4) Alt=$(echo $line | sed 's/ /\t/g' | cut -f 5 ...
written 13 days ago by A3.7k
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Comment: C: Is this range of VAF is ordinary?
... Actually somebody wrote a script for me; Assuming a Strelka .vcf for SNV #Basic information chrom=$(echo "$line" | sed 's/ /\t/g' | cut -f 1) #&& echo $chrom; Pos=$(echo "$line" | sed 's/ /\t/g' | cut -f 2) #&& echo $Pos; Ref=$(echo "$line" | sed 's/ /\t/g' | cut -f ...
written 14 days ago by A3.7k
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Is this range of VAF is ordinary?
... Hi I have calculated `Variant Allele Frequency (VAF)` for called SNVs and INDELs called by Strelka separately. For getting VAF, I done VAF = Tumour Variant Allele Count / Tumour Read Count For some position of the genome I have `VAF > 30` , so DOES these big VAFs are normal or I am doing ...
vcf wgs vaf written 14 days ago by A3.7k
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Comment: C: Some interpretation of Strelka output
... Thank you I read all you kindly posted but still not quite sure should I use Alternate or indel allele in this formula? Somatic allele freqeuncy is $tier1AltCounts / ($tier1AltCounts + $tier1RefCounts) ...
written 17 days ago by A3.7k
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Some interpretation of Strelka output
... Hi I have called INDELs for tumor/matched normal by Strelka caller In .vcf header I have ##FORMAT= ##FORMAT= I want to calculate VAF, so I am confused by the difference of `alternate allele` versus `indel allele` ; Which one I should use for calculating Variant Allele Frequency (VAF)? ...
indel wgs strelka written 17 days ago by A3.7k • updated 17 days ago by ATpoint28k

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