How to work with Low allele Depth Variants in Strelka Variant caller
When using Strelka on sequenced bams, the VCF file contains many variants with very low allelic depth.
When I try to sequence the sample again and then generate the VCF there is a lot of mismatch between the 2 generated VCFs. This problem occurs at high frequencies in variants with low allelic depth ( 1, 2) and steeply drops off above this limit to almost non-existent.
When considering these Variants, should we ignore or filter out variants with low allelic depth?
Has anyone else encountered this issue and how did you deal with this issue?
• 603 views
•
link
updated
by
Ram
•
written
by
abhishekghadge •
•
written
by
abhishekghadge •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Handling high missingness when merging single-sample VCFs
written by SeoG •
-
Multiple unique reads sharing same UMI barcode
written by ww22runner •
-
vcf variant selection
written by ethan.kreuzer •
-
PoolSNP RuntimeError: dictionary changed size during iteration
written by shpak.max •
-
'map' error sequenza from Strelka vcf.somatic.snvs in python 3.8 and tier 1 or 2?
written by heetak.lee •
-
Remove variants that do not map to human genome
written by john.michel.rouhana •
-
bbmap callvariants - how to add sample names, how to get 0/0 alleles back?
written by Philipp Bayer
-
annotating TCGA VCF file
written by jan
-
Allelic Depth 1000 Genomes call set
written by QVINTVS_FABIVS_MAXIMVS
-
Strelka Indel Allele Counts
written by Richard
