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

Hi all, is it possible to convert all VCF data to forward strand? Is there a script that can do that?

Thanks again in advance.

vcf
• 1,902 views • link
updated by Ram 4.5K • | written by win 100

how did you get a VCF on the reverse strand ?

• 1 views • link
written by Pierre Lindenbaum 17K

The DP4 field under INFO contains the information for reads covering the strand for ref and alt bases. If you manipulate this field as per your requirement, you can get it.

Plz elaborate your question, so that we write the code for it.

• 1 views • link
updated by Ram 4.5K • | written by Renesh 221

0 answers

No answers yet.

Log in to answer this question.

More posts like this
  • ClinVar local install
    written by win 100
    Hi all. I want to do downstream analysis of VCF files and need to interface my data with ClinVar. I found ClinVar in VCF format …
  • Lift-over on a VCF
    written by win 100
    <p>Hi all,</p> <p>I have a VCF file that was generated using HG18 and I want to convert it to VCF but that has HG19 data.</p> …
  • Individual VCF files from main VCF file
    written by win 100
    Hi all, In the 1000 genomes project there is one large VCF file which has all the samples represented in columns. I want to generate …
  • Convert GVF to VCF
    written by win 100
    Hi all. Does any know of a script or code that can convert a GVF file to VCF? There is a reference to a link …
  • Reference file name from VCF file
    written by win 100
    Hi all, is it possible to determine the name of the reference file used from any VCF file? Thanks in advance.
  • Venter Genome Vcf
    written by win 100
    <p>Hi all, I was wondering if there was a VCF version of Venter's genome? There is a GFF file but not sure if there was …
  • Overlap Between Array And Vcf
    written by win 100
    <p>Hi all, Hope someone can help. I have a tab delimited file of microarray data and a VCF file of the same sample. I want …
  • Vcf Database Table Structure
    written by win 100
    <p>hi all, I am trying to store VCF files in a database table. While the VCF file structure is quite straight forward the issue I …
  • Create A Tbi File From Vcf
    written by win 100
    <p>hi all. i am generating a vcf file as the end result of my processing and i want to perform an interval query. since, tabix …
  • Snp Ambiguous Alleles
    written by win 100
    <p>Hi there, Hoping someone can help. I have sequences from -ve strand and i also have the reference and variant alleles at certain location on …