Blat Input From Vcf File

Question

[GPR]

Hello, I want to do a BLAT alignment on the SNPs I got in my analysis. My VarScan output is in vcf format. Any hints at how to convert a vcf file to one amenable to input in BLAT? Thanks, G.

[Matt Shirley]

You might want to consider explaining why you need to align variant calls to a reference genome. Are you trying to visualize the location of your variants? If so, you might consider using something like IGV and loading your aligned reads and vcf.

[GPR]

I want to identify alignments to paralogous genes and eliminate these, to filter out potential false positive calls in my analysis.

Answer 1

[gs]

I don't know BLAT, what shall it look like ? I'm just reading/converting the 1000 genomes/.../omni vcf-files

testing how to post here

--------edit-------------

OK, http://en.wikipedia.org/wiki/BLAT_(bioinformatics)

------------------edit------------------

downloaded blat ...

blat - Standalone BLAT v. 33x5 fast sequence search command line tool usage: blat database query [-ooc=11.ooc] output.psl where: database and query are each either a .fa , .nib or .2bit file,

or a list these files one file name per line.

so, convert .vcf to fasta ? that's what I'm currently doing ... (but considering the SNP positions only to reduce the size)

but why align the fasta with blat then ? It should be aligned, - same positions for the sequences in the vcf

... unless you want to merge two vcfs with different positions ?!?

Answer 2

[Liping]

One possible solution to this is:

You extract flanking sequences of all your SNVs in your VCF file with the BEDtools, and then do a BLAT alignment on the flanking sequences.

1. grep -v -e '^#' your.vcf | awk 'BEGIN{OFS="\t"}{print $1,$2-50,$2+50,$1 ":" $2}' >try.bed
2. bedtools getfasta -fi ucsc.hg19.fasta -bed try.bed -fo VCF_SNVs.fasta -name
3. blat ucsc.hg19.fasta VCF_SNVs.fasta output.psl

[GPR]

Will try this. Many thanks. G.

Answer 3

[GPR]

I want to identify alignments to paralogous genes and eliminate these, to filter out potential false positive calls in my analysis. Thanks for your help. G.