Manta SV (specially Translocation) · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

Manta SV (specially Translocation)

Hi Everyone!

I have manta generated and VEP annotated vcf file for tumor vs normal. In my data there are lot of translocations in comparison to DUP/DEL/INV/INS. I would like to know how to find true translocations. I was trying to filter using PR:SR ratio > 10 (tumor) and PR:SR < 10 (control) and keep one translocation.

chr1    3855261 A   ]chr5:124764103]A   BND 8,0:48,0    10,1:49,3
chr5    124764103   C   C[chr1:3855261[ BND 8,0:48,0    10,1:49,3

First is for Control 8,0:48,0 tumor sample 10,1:49,3

Please guide me to consider the true translocations and why does my data have more translocations. I request you to help me to find true positive translocation

manta structural-variant

• 551 views • link

updated 1.4 years ago by Ram

• written 1.4 years ago by Nai •

0 answers

No answers yet.

Log in to answer this question.

More posts like this

FORMAT column with GT for somatic SV VCFs
written 3.1 years ago by Christian •

Hi, I have done tumor-only somatic structural variant (SV) calling with Manta. This results in several VCFs with candidate variants. However, some of these do …
How to Update/Edit INFO field of VCF
written 5.9 years ago by AISHA

Hi all, I intend to convert a bed file of structural variants to VCF, keeping all the fields in bed file (except target_name and target_start) …
bcftools filtering on INFO fields
written 6.1 years ago by Stephane Plaisance

below is a piece of my VCF where I try to extract rows with SUPPORT>10 but fail to specify such filter. I tried: `bcftools filter …
Annotating variants called with NanoVar with Annovar
written 6.6 years ago by asmariyaz23 •

Hello, I am trying to annotate SVs that I got by running NanoVar using Annovar (build hg38). Here are the commands I used to run …
Variant calling pacbio bacteria
written 7.0 years ago by firestar

I have PacBio reads from three bacterial genomes as three samples. They were de-novo assembled using HGAP4 and polished. One of samples was taken as …
structural variants in gnomad and the VCF spec. Why is tabix/bcftools failing ?
written 7.1 years ago by Pierre Lindenbaum

I downloaded the SV from gnomad: wget -O gnomad_v2_sv.sites.vcf.gz "https://storage.googleapis.com/gnomad-public/papers/2019-sv/gnomad_v2_sv.sites.vcf.gz" wget -O gnomad_v2_sv.sites.vcf.gz.tbi "https://storage.googleapis.com/gnomad-public/papers/2019-sv/gnomad_v2_sv.sites.vcf.gz.tbi" First, an observation. For BND, the END value is used in …
Run Delly by chromosome
written 7.4 years ago by tg25 •

Dear All, How do you run Delly by chromosome? I have looked at the [Delly GitHub page][1] and I cannot find the answer. I have …
What are the strands of structural variant breakpoints?
written 8.0 years ago by weishwu •

I'm trying to use a tool named ShatterSeek to call chromothripsis regions from SV calls. It requires me to list the breakpoint strands for each …
DELLY SNV detection output intrepetation
written 8.0 years ago by mks002

Dear all, I have performed SNV calling on plasmodium samples. However I am facing some difficulty to interpreting certain fields. I wish to annotate this …
Finding overlapping regions in two file along with their associated information
written 8.1 years ago by BAGeno

Hi, I have two file in which there are chromosomes positions and other information. I want to find their overlapping regions for this purpose I …