Questions tagged [filtering]
The filtering tag has no usage guidance.
7
questions with no upvoted or accepted answers
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135
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Empty values in FILTER field after running Mutect2
I was expecting something like in this image:
But when I ran Mutect2, the FILTER field was empty in the output VCF file. How can I enable PASS filters?
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1
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0
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33
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RNAseq SNP discovery: deciding upon filters and dealing with allele expression bias
I am working with non-model plant RNA samples which we have been deep sequenced and analysed using STAR aligner under default parameters.
Aim We would like to conduct SNP discovery of these samples.
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1
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23
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Discard Candidates if N >= 40%
I have obtained ( interspersed repeats ) libraries in the Palm plant genome. Still, unfortunately, the candidates obtained seems false positive a lot of tandem repeats found, due to denovo ...
- 364
1
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33
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Filtering pileup from site lists
I want to write a script that filters a pileup file from a site lists file.
As an input I get a reference genome, pileup and site lists files.
Example of an output for this script:
Pileup File :
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1
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38
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ExpressionSet with a custom gene list
After an ExpressionSet is established,
I want it to contain only the genes of my choice ("selected.txt")
What is the best approach??
Thanks
- 11
1
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0
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248
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Error filtering SNPs with Plink
Im trying to filter SNPs using PLINK with this command. Also, the .map and .ped files were converted to a plink format from a vcf file (...
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652
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Filtering samples by FORMAT attributes using bcftools
The -e and -i options of the bcftools filter command appear, by default, to only allow for ...
- 101