Questions tagged [genomics]

Genomics is an interdisciplinary field of science focusing on the structure, function, evolution, mapping, and editing of genomes.

Filter by
Sorted by
Tagged with
6 votes
3 answers

Somatic tumor only variant calling?

I'm evaluating possibilites for somatic tumor variant calling without paired-normal samples. I'm aware of the consequences without a normal sample. All the popular variant calling tools such as ...
SmallChess's user avatar
  • 2,739
20 votes
1 answer

The state, limitations and comparisons of large variant stores

Background: We're increasingly needing some way of storing lots of variant data associated with lots of subjects: think clinical trials and hospital patients, looking for disease-causing or relevant ...
agapow's user avatar
  • 788
7 votes
1 answer

ethnicity check either from bam or vcf files

What tool could I use to check the ethnicity of a human bam or vcf file? I would like to use the results as a QC check to know whether a given sample or set of samples match the ethnicity information ...
719016's user avatar
  • 2,324
2 votes
1 answer

Difference between bioinformatics and cheminformatics [closed]

Anyone can answer, and should be in simple way
Harsha's user avatar
  • 29
2 votes
0 answers

STACKS: process_radtags only reads 1 input file and returns >90% barcode not found drops

I am trying to demultiplex some paired-end ddradseq data and am running into an issue with STACKS in that the program only seems to read 1 of my files for input (there are 2) and also results in over ...
heather_l's user avatar
1 vote
2 answers

Transcription factor targets for Human and Mouse genes

I want to get transcription factor targets for my list of genes (For Human and Mouse) I have found ENCODE Transcription Factor Targets database (The link is given below). But I am looking for some ...
Priya's user avatar
  • 351
0 votes
1 answer

what is the most complete vcf file of population allele frequencies that can be built/downloaded from public datasets?

What is the most complete vcf file of population allele frequencies that can be built/downloaded from public datasets nowadays? About 5 years or so ago, it used to be the latest release of the CSHL ...
719016's user avatar
  • 2,324