Calling CNVs without a normal
Hi all,
Is there a way to call CNVs without a matched normal? I have a tumor sample and a panel of normals and a reference, but no matched normal. I understand that the CNVs won't be somatic but is there a way to just get CNVs with respect to a reference?
1 answer
CNVkit works well with a reference sample (or pool of normals to create one from). Yes, they aren't somatic, but it does what you want. Also very easy to use.
• 0 views
•
link
written
by
jared.andrews07
Log in to answer this question.
More posts like this
-
Which type of variant caller should I use in a WES normal cell line sample?
written by bompipi95 •
-
Calling CNVs using a single tumor sample
written by vctrm67 •
-
Somatic variant calling mutect2 tumour only
written by cellulebioinfobiscem •
-
Variant calling on matched primary and metastatic tumor without normal samples.
written by Venados •
-
Panel of tumors for CNV detection
written by biobiu
-
Whole Exome Sequencing Depth
written by bioinfonerd •
-
Strategies to call variants from a cancer sample
written by John Ma
-
CNVkit calling strategies with matched-normal tumor
written by fbrundu
-
Concept of Matched normal vs. Virtual Normal
written by sutturka
-
Calling variants in blood tumor samples without matched normal samples
written by umn_bist •
try manta, lumpysv, etc...
These seem like they're for SV analysis, not CNV?
CNV= DEL= SV CNV= DUP/INS = SV
idk, for me calling CNVs in cancer automatically mean "clonal decomposition" also - and SV callers dont do this (as well as inference of actual copy-numbers), also SV callers struggle with non-tandem duplications
however, without matching normal this task become close to impossible (without B-allele frequencies mainly) - it is not realistic to decompose CNVs into 2 alleles with different copy-numbers and estimate clonal cell fraction for each event...