Generate head on vcf file from freebayes
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6.4 years ago

well after medhat told me my vcf doesn't have header I try to figure out how to get it, my vcf file I got it with two ways

bin/freebayes --fasta-reference /media/cri/CRIS_DATA/ULT/OTRO2/otro/hg19.fa /media/cri/CRIS_DATA/ULT/OTRO2/otro/input.header.realigned.bam >/media/cri/CRIS_DATA/ULT/OTRO2/otro/freebayessample3.vcf


bin/freebayes --min-coverage 10 -V -f /media/cri/CRIS_DATA/ULT/OTRO2/otro/hg19.fa /media/cri/CRIS_DATA/ULT/OTRO2/otro/input.header.realigned.bam >/media/cri/CRIS_DATA/ULT/OTRO2/otro/freebayessample.vcf

Is any command to add to get my head on the file?

Thanks

vcf • 1.5k views
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FreeBayes outputs VCF headers by default (at least, the current version does). Are you sure the VCF with missing header is direct output from FreeBayes, or after additional processing (e.g., BEDtools 'subtract' removes headers)?

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from the documentation page the command is

freebayes -f ref.fa aln.bam >var.vcf

and it should have the header by default what was the command you used for the alignment and is it was to the same reference

/media/cri/CRIS_DATA/ULT/OTRO2/otro/hg19.fa

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