Questions tagged [filtering]

The tag has no usage guidance.

7 questions with no upvoted or accepted answers
Filter by
Sorted by
Tagged with
2 votes
0 answers
135 views

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? ...
user avatar
1 vote
0 answers
33 views

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. ...
user avatar
  • 11
1 vote
0 answers
23 views

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 ...
user avatar
  • 364
1 vote
0 answers
33 views

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 : ...
user avatar
1 vote
0 answers
38 views

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
user avatar
  • 11
1 vote
0 answers
248 views

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 (...
user avatar
0 votes
0 answers
652 views

Filtering samples by FORMAT attributes using bcftools

The -e and -i options of the bcftools filter command appear, by default, to only allow for ...
user avatar