Combine REF/ALT alleles from VCF with extracted flanking sequences

Question

[wrengs]

Hi,

I have recently used bedtools flank in combination with getfasta to extract sequences flanking some structural variants, using a VCF file and genome file.

Link to the VCF file: ftp://ftp.solgenomics.net/genomes/tomato100/March_02_2020_sv_landscape/variants/LYC1969.ont.v1.0.s.vcf.gz

Link for the SL4.0 genome fasta: ftp://ftp.solgenomics.net/genomes/Solanumlycopersicum/assembly/build4.00/

For the first structural variant (ID = 261_0_1), 20bp flanking sequences were extracted:

Info from VCF file: POS ID REF ALT 19623 261_0_1 ATATATATATATATATATATATATATATATATATA A

Output from bedtools flank: SL4.0ch01 19602 19622

SL4.0ch01 19658 19678

Output from bedtools get fasta:

SL4.0ch01:19602-19622 GAATGTATTCATATATATAT

SL4.0ch01:19658-19678 TAAAATTCTAACTTGAGAAA

I was wondering if somehow the extracted flanking sequences could be combined with the REF and ALT alleles from the VCF, i.e. using a tool, in the following output:

261_0_1 GAATGTATTCATATATATAT[ATATATATATATATATATATATATATATATATATA/A]TAAAATTCTAACTTGAGAAA

Of course, for just a single structural variant I could do this manually. However, my intention is to do this with some thousands of structural variants in combination with multiple VCF files.

Many thanks!

Answer 1

[Pierre Lindenbaum]

I wrote http://lindenb.github.io/jvarkit/Biostar251649.html for Annotating the two flanking bases of SNPs in a VCF file (perhaps SnpEff?) . May be you can use this to annotate your VCF with the flanking sequences....

see also: Extract SNPs flanking sequences based on VCF and genome Fasta files