How to Update/Edit INFO field of VCF

Question

[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) in INFO column of VCF. For that, I used SURVIVOR software which didn't completely served the purpose.

Is there a method/software which can be used to specifically update/edit INFO column of VCF based on the given bed file..?

Example bed record:

target_name target_start    target_end  sv_type sv_length   query_strand    query_name  query_start query_end   query_length
chrX    153022091   153022244   deletion    153 -   XYZ 63364   63364   335065

Here is the output of SURVIVOR:

##fileformat=VCFv4.1
##source=SURVIVOR
##ALT=<ID=DEL,Description="Deletion">
##ALT=<ID=DUP,Description="Duplication">
##ALT=<ID=INV,Description="Inversion">
##ALT=<ID=BND,Description="Translocation">
##ALT=<ID=INS,Description="Insertion">
##INFO=<ID=CHR2,Number=1,Type=String,Description="Chromosome for END coordinate in case of a translocation">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the structural variant">
##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Precise structural variation">
##INFO=<ID=SVLEN,Number=1,Type=Float,Description="Length of the SV">
##INFO=<ID=SVMETHOD,Number=1,Type=String,Description="Vector of samples supporting the SV.">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of the SV.">
##INFO=<ID=STRANDS,Number=1,Type=String,Description="Indicating the direction of the reads with respect to the type and breakpoint.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  Sample
chrX    153022092   DEL00BED    N   <DEL>   .   PASS    IMPRECISE;SVTYPE=DEL;SVMETHOD=BEDFILE;CHR2=chrX;END=153022244;CIPOS=0,0;CIEND=0,0;SVLEN=152 GT  ./.

Thanks in advance!

Best wishes

[Ram]

Have you looked at bcftools annotate? What are some other tools you've tried and run into specific problems with?

Answer 1

[d-cameron]

You won't find a tool that works on your input as your input does not comply with the UCSC BED file format, nor the BEDPE format. At best, it's a BED3 file.

Here is the output of SURVIVOR:

Do you require VCF for your downstream analysis? Specically, do you require the output match your SURVIVOR example?

Be aware that the SURVIVOR output you have described is not compliant with the VCF specifications on how SVs are represented. Specifically, the CHR2, PRECISE, and STRANDS fields are not part of the VCF SV specifications. See Section 4.1 of the specifications to see how interchromosomal rearrangements should be specified.

TLDR: You're not going to find a tool that works with your custom data format - you'll need to write a simple conversion script yourself.