Hi,
I filter variants from a WGS data with different databases like genomicSuperDups. However, many variants (more than 70%) get filtered by genomicSuperDups. As it is not normal, how is it possible to find out why so many variants get filtered? The problem is that annovar provides a list of dropped variants for different filters except genomicSuperDups. So there is no way to find out the variants that get filtered by this db.
another question is that if snp129 is more clean than snp137 in using snp137NonFlagged,snp137?
variants_reduction.pl myfile -protocol genomicSuperDups,1000g2012apr_all,snp137NonFlagged,snp137,dgv -buildver hg19 humandb/ -operation r,f,f,f,r -aaf_threshold .01 -remove
NOTICE: Processing operation=r protocol=genomicSuperDups
NOTICE: Running step 1 with system command <annotate_variation.pl -regionanno -dbtype genomicSuperDups -buildver hg19 -outfile myfile.step1 myfile.step0.varlist /humandb/>
NOTICE: Reading annotation database humandb/hg19_genomicSuperDups.txt ... Done with 51599 regions
NOTICE: Finished region-based annotation on 2033 genetic variants in myfile.step0.varlist
NOTICE: Output files were written to myfile.step1.hg19_genomicSuperDups
NOTICE: After step 1, 61 variants are left in analysis.
-
Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?
Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating...10-14-2026, 09:55 AM -
Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...