User: ajuiwl

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ajuiwl30
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Posts by ajuiwl

<prev • 9 results • page 1 of 1 • next >
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Consensus VCF file from several variant callers
... Hi all, I want to do a consensus VCF file with only the variants that have been called by two variant callers. The problem is that for the same variant the INFO and FORMAT columns of the VCF files show different values, this is to say: GATK shows the variant with DP, MQ, FS values that differ from t ...
vcf variant calling freebayes gatk written 5 weeks ago by ajuiwl30 • updated 5 weeks ago by Pierre Lindenbaum116k
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Comment: C: Filter VCF with bash commands
... That is true, I just found that there are some variants in the vcf that didn't have INFO about QD nor DP, and the commands I did didn't considered this. So I agree with you using already made software in that sense. In addition I will add that sometimes you are working in a server that requires the ...
written 10 weeks ago by ajuiwl30
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Comment: C: Filter VCF with bash commands
... Some programs change the way variants are normalized, the header, require installations, require dependencies, and other issues that bash code can avoid, moreover I have more control over what I do. ...
written 10 weeks ago by ajuiwl30
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Comment: C: Filter VCF with bash commands
... This answer does not consider decimal positions, in the way that 8.1 won't be kept. ...
written 10 weeks ago by ajuiwl30
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Answer: A: Filter VCF with bash commands
... Thank you for your answers, I found the way of doing it with: grep -Po 'QD=.*' $FILE | cut -d";" -f1 | sed -r 's/[QD\=]//g' | paste -d'\t' $FILE - | awk 'BEGIN{OFS="\t"}{if ($11>8) {$11=""; print}}' ...
written 10 weeks ago by ajuiwl30
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Filter VCF with bash commands
... Hi, I have been trying to manually filter a vcf file by QD score, but I have not been able to do it properly. I thought of using awk and indicate that a specific field has a value greater than 8 (that is the value I want to filter it), but I have records where the QD variable does not occupy the sam ...
vcf grep awk bash written 10 weeks ago by ajuiwl30 • updated 10 weeks ago by dariober9.8k
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DP and DP at site do not match using only 1 sample in VCF
... I only used 1 sample with BWA and GATK4 germinal variants. The final VCF has variants like this: 1 230451938 . G A 18.25 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.967;ClippingRankSum=0.00;DP=20;ExcessHet=3.0103;FS=4.771;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.0 ...
vcf variant calling gatk written 3 months ago by ajuiwl30
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Comment: C: 4/6 genotype in VCF
... Thank you for the answers, the fact that I do not understand is how the calling in a diploid genome can yield variants with more than 3 alternative alleles (reference, copy 1 and copy 2) if only 1 sample is being used, is that possible? ...
written 3 months ago by ajuiwl30
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4/6 genotype in VCF
... Hi all, I have been doing variant calling analysis in human cancer exomes and some variants in the VCF file have genotype like 4/6 or 2/3, is there any explanation for this fact, since I expected to see only 0/1, or 1/1? Thank you very much ...
vcf variant calling genotype written 3 months ago by ajuiwl30 • updated 3 months ago by Pierre Lindenbaum116k

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Scholar 10 weeks ago, created an answer that has been accepted. For A: Filter VCF with bash commands

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