Extract svtype from svaba · Biostar

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

Extract svtype from svaba

Hi All,

I have a question for people familiar with sbava caller. I noticed that all structural variant types detected by this tool are considered as BND. Do you have an idea how to make the DEL, IND classifications appear in the vcf (I asked this question in the svaba github issues but given the response time I asked the question again here).

Note: I work on germline variants.

Thanks in advance

sv vcf svtype svaba

• 743 views • link

written 4.5 years ago by Adham •

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 …
Tuning seurat integration strength to prevent overcorrection
written 3.9 years ago by nhaus •

Hello, I am currently working with multiple replicates for 2 different conditions (stimulated and unstimulated cells) that I want to integrate to adjust to correct …
How to ignore "GT" from vcf file
written 5.5 years ago by SUDOsundu •

I used medaka_haploid_variant caller to identify variants in my viral reads. After running medaka tools annotate, I got an annotated vcf file. Then filtering by …
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 …
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 …
Are the somatic mutations in TCGA filtered for germline mutations?
written 7.5 years ago by rafi.zon •

Hi, I read from somewhere an answer [Question: How do I get germline mutation data from TCGA][1] that the germline mutations are filtered from the …
how to distinguish mosaicism out of germline de novo mutations
written 8.5 years ago by lait

In our trio data, we have identified germline denovo mutations in the child using a bioinformatics pipeline that we have 'assembled'. In general, some of …
FreeBayes Variant Diversity capture
written 8.6 years ago by shubhra.bhattacharya

I have used FreeBayes for variant calling after facing some issues with GATK. The bam file which FreeBayes requires as a mandate is 53 Gb …
Strategies to call variants from a cancer sample
written 8.7 years ago by John Ma

Hi all, I am looking to identify DNA-level variations from a matched tumor-normal WES data. Specifically, I just want to know the variations in the …