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Recent Replies
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A: Where to start? Newbie trying to enter the world of computational biology gettin by
Mensur Dlakic • 8.1k
It is not a simple question at all, especially if you have no idea about this type of research. I...
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C: About GATK4 Mutect2 runtime (Whole Exome seq) by
kwanghoon • 20
gatk Mutect2 -R $HG38 --native-pair-hmm-threads 32 -I input.bam -O unfiltered_output.vcf Thi...
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C: About GATK4 Mutect2 runtime (Whole Exome seq) by
_r_am ♦ 32k
That's odd. Can you add your entire Mutect2 command in a comment below?
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C: About GATK4 Mutect2 runtime (Whole Exome seq) by
kwanghoon • 20
Thank you!! That sounds relief to me..
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C: About GATK4 Mutect2 runtime (Whole Exome seq) by
kwanghoon • 20
That sounds relief to me. I open .vcf file there are no values at column Qual, Filer like below....
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C: About GATK4 Mutect2 runtime (Whole Exome seq) by
MatthewP • 850
I am running WGS on my local linux server each sample needs 28 hours Mutect2. Human sample.
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C: About GATK4 Mutect2 runtime (Whole Exome seq) by
_r_am ♦ 32k
6 hours per sample doesn't sound like much time at all, but time is rarely a measure of output qu...
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C: GSVA Error: "Less than two genes in the input expression data matrix" by
_r_am ♦ 32k
In that case, I'd recommend using `read.table`. Code is already difficult to remember and compreh...
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swbarnes2 ♦ 9.4k
With only three replicates, you can't omit that sample based solely on your visualizations. Now,...
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nextflow (not tested) params.ref="/media/gatk/Homo_sapiens_assembly38.fasta" params.bams...
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Yes, I believe some methods result in further normalisation / transformation. This information ca...
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use a workflow manager.
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