GATK VCF to BED
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Adrian Johnson
Mar 15, 2011, 1:33:10 PM3/15/11
to bedtools...@googlegroups.com
Hi:
How can I convert GATK VCF file to a bed file. Is there a
functionality in BedTools, to do such conversion. Any help
appreicated.
thanks
Adrian
How can I convert GATK VCF file to a bed file. Is there a
functionality in BedTools, to do such conversion. Any help
appreicated.
thanks
Adrian
Vladimir Grubor
Mar 15, 2011, 1:57:37 PM3/15/11
to bedtools...@googlegroups.com
cat your_file.vcf |tail -n +12 |awk '{FS="\t";OFS="\t";print $1,$2-1,$2,$3, etc}' >your_file.bed
where:
tail removes the first 11 lines of the vcf header - change it to the number that suits you
Cheers,
Vlad
where:
tail removes the first 11 lines of the vcf header - change it to the number that suits you
Cheers,
Vlad
2011/3/15 Adrian Johnson <orioleb...@gmail.com>
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