combine CNV calls from different softwares
Hi guys
I have generated CNV calls from PennCNV, R-Gada and QuantiSNP. I would like to generate a consensus of these CNVs by merging them and only keep those that was detected by at least 2 methodes. Is there a software that can handle the different formats and generate the desired output? Otherwise, any other suggestion is appreciable.
Thanks :)
• 2,585 views
•
link
updated
by
s.awasthy •
•
written
by
Myosotis1979 •
•
written
by
Myosotis1979 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Merging multiple samples Copy number variation file and annotating
written by Anitha •
-
vcf procesing for ML antigen prediction
written by Javier •
-
Comparing SV calls produced by VG call on a Minigraph-Cactus produced Pangenome Graph vs. a linear …
written by peterdfields •
-
Forum: Best practices for merging vcfs with different positions + different samples?
written by pabe •
-
How to handle VCFs from the same sample but using different aligners and variant callers?
written by aldhairmedico •
-
detecting overlapping CNV from 2 algorithms
written by Myosotis1979 •
-
Effect Of Undetected Genes On Ontology Analysis
written by dario.garvan
-
Plink Cnv Map Names
written by bob.obr13n •
-
Extracting Variants For Select Individuals Overlapping Pre-Specified Regions From 1000 Genomes
written by Ryan D
-
Cnv Calling Methods For The Illumina Omni2.5 - Penncnv And Quantisnp Possible?
written by Ryan D
A good starting point would be to paste some output that you have from each program. In short, yes, there are most certainly customised ways of meta-analysing the output from these programs.