User: rturba07

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rturba070
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Posts by rturba07

<prev • 5 results • page 1 of 1 • next >
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Answer: C: GATK 3.8.0 VariantFiltration ERROR input string
... Ah, I've found out the reason for that here: https://github.com/broadinstitute/gatk/issues/5582. I hope this helps others as lost as me! I did not realize the INFO fields could have "NaN" values. Solution to fix is: bcftools view in.vcf.gz | sed 's/=nan/=NaN/g' | bgzip > fixed.vcf.g ...
written 4 weeks ago by rturba070
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GATK 3.8.0 VariantFiltration ERROR input string
... Hello, I am running GATK 3.8 on a Linux cluster. I am trying to run the tool VariantFiltration with the following commands: java -jar $GATK/GenomeAnalysisTK.jar \ -T VariantFiltration \ -R $ref \ -V $wd/vcf/filtered/stick84_SNPs_GATK.vcf \ --filterExpression "QD ...
genome software error snp written 4 weeks ago by rturba070
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Comment: C: error with running distruct.py in fastSTRUCTURE
... I'm having the exact same issue. Have you figured out why? ...
written 5 months ago by rturba070
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Comment: A: Find particular SNPs affecting PCA
... I'm sorry. This is my first time doing this kind of analysis, and I don't understand how the structure of your PCA object looks like. I'm using the SNPRelate package to do my PCAs, and the loading object looks like this: List of 8 $ sample.id : chr [1:3893] "AF346967.1" "AF346968.1" "AF346 ...
written 6 months ago by rturba070
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Comment: C: How can I obtain a list of SNPs generating clusters in a PCA?
... I'm sorry. This is my first time doing this kind of analysis, and I'm still having trouble on how to do this. I've tried looking all over. How can I extract the loadings for the PC that I want with its associated snp.id? And how is this different from the snp correlation analysis [from this tutorial ...
written 6 months ago by rturba070

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Scholar 4 weeks ago, created an answer that has been accepted. For C: GATK 3.8.0 VariantFiltration ERROR input string

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