Hello,
Sometime back, I had asked for help regarding the conversion for the vcf format
to bed format for liftOver. But unfortunately, that did not work for me.
My vcf format goes like this
##fileformat=VCFv4.1
##samtoolsVersion=0.1.16 (r963:234)
.......
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
sample1 sample2 sample3 sample 4
chr1 11457 . C G 49.7 .
DP=3;AF1=0.9999;CI95=0.375,1;DP4=0,0,0,3;MQ=49;FQ=-29.3 GT:PL:GQ
1/1:4,3,0:39 1/1:40,3,0:39 ...
I used the awk command
grep -v "^#" input.vcf | awk '{printf
"%s\t%d\t%d\t%s|%s|%s|%s|%s|%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n",
$1,$2-1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,$13,$14,$15}' > output.bed
Now when I tried to use it for the liftOver , I get an error saying
>./liftOver output.bed hg19ToHg18.over.chain.gz new.bed unMapped
Reading liftover chains
Mapping coordinates
Expecting integer field 7 line 1 of output.bed, got 1/1:40,3,0:39
I need to retain GT:PL:GQ values as I would need it for my further analysis.
Is there any way out of this ? Any suggestions would be appreciated..
Thank you,
Warm Regards,
Nandini
> > Date: Tue, 2 Aug 2011 10:06:23 -0700
> > From: [email protected]
> > To: [email protected]
> > CC: [email protected]
> > Subject: Re: [Genome] liftover hg19 to hg18
> >
> > Good Morning Nandini:
> >
> > You can convert your VCF files to bed format.
> >
> > If your VCF files follow the format:
> > http://www.1000genomes.org/node/101
> >
> > This awk command will convert them to bed format (assuming | is not a
> > character found in the vcf fields):
> >
> > grep -v "^#" yourFile.vcf | awk '{printf "%s\t%d\t%d\t%s|%s|%s|%s|%s|%s\n",
> > $1,$2-1,$2,$3,$4,$5,$6,$7,$8}' > yourFile.bed
> > liftOver yourFile.bed hg19ToHg18.over.chain newFile.bed unMapped
> >
> > Then, from that lifted bed file back to vcf:
> >
> > awk '{printf "%s\t%d\t%s\n", $1,$2+1,$4}' newFile.bed | tr '[|]' '[\t]' >
> > newFile.vcf
> >
> > You may need to adjust these awk statements depending upon the exact format
> > of your vcf file.
> >
> > --Hiram
> >
> > Nandini B wrote:
> > > Hello,
> > > I am trying to use liftover for my SNPs from hg19 to hg18. But I have my
> > > SNP files in either gff3 format or vcf (v4.1). Is it possible to use
> > > these files to execute the command
> > > liftOver -gff oldFile.gff3 hg19ToHg18.over.chain newFile.gff3 unMapped or
> > >
> > > liftOver -vcf oldFile.vcf hg19ToHg18.over.chain newFile.vcf unMapped
> > >
> > > Or do I have to convert them into BED format, if so, is there any tool
> > > that could do this ?
> > >
> > >
> > > Thank you,
> > > Warm Regards,
> > >
> > > Nandini Badarinarayan
>
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> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
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