structural variant vcf file comparison
Hi,
I have six vcf files (cases vs control) that contain structural variants with variable length from nanopore sequence run. These vcf files were generated using NGMLR aligner followed by sniffle.
What is the best way/tool to compare these files?
Thanks Tarek
• 3,508 views
•
link
updated
by
WouterDeCoster
•
written
by
tarek.mohamed
•
written
by
tarek.mohamed
1 answer
You can merge these SV vcf files using SURVIVOR, in which you can specify a distance to allow some variability between breakpoints.
• 0 views
•
link
written
by
WouterDeCoster
Log in to answer this question.
More posts like this
-
News: Course: Structural Variant Detection and Comparison
written by Physalia-courses
-
Problem in merging multiple samples VCF file obtained from Structural variant caller Lumpy
written by sardana.thakur.prachi •
-
Comparative analysis of NGS platforms for data analysis
written by hussaindilawar33 •
-
Efficiently detect Structural Variant
written by its.roops •
-
Are reads with the same length and position always "duplicates"
written by elcortegano
-
Extract VCF from genome assemblies of multiple individuals
written by Anand Rao
-
Nanopore SNP and indels calling tool
written by tarek.mohamed
-
Symbolic alternate allele in the VCF ALT field
written by tsimakova •
-
Why VarScan cannot call variants which appear in 1000genome
written by sxl919 •
-
Checking kinship coefficients and relationships and comparing genotyping data to exomes
written by DG
