Question: How to convert genomic region of following type to vcf file?
0
gravatar for svp
8 months ago by
svp420
Bangalore
svp420 wrote:

I have list of genomic co-ordinates as follows:

chr7:g.87053221C>T
chr9:g.133738306G>A
chr9:g.133738309A>G
chr9:g.133738325T>C
chr9:g.133738330A>G
chr9:g.133738340A>G
chr9:g.133738342C>G

I need to convert this to a vcf file and perform liftover to Grch38 coordinate? Are there any tools or codes available to perform this?

liftover conversion vcf • 217 views
ADD COMMENTlink modified 8 months ago by Pierre Lindenbaum134k • written 8 months ago by svp420
2
gravatar for Pierre Lindenbaum
8 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum134k wrote:
tr ":.>" "\t" < input.txt  | sed -r 's/([0-9]+)([ATGC]+)/\1\t\2/' | awk  'BEGIN{print("##fileformat=VCFv4.2");print("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO");} {printf("%s\t%s\t.\t%s\t%s\t.\t.\t.\n",$1,$3,$4,$5);}' 
##fileformat=VCFv4.2
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO
chr7    87053221    .   C   T   .   .   .
chr9    133738306   .   G   A   .   .   .
chr9    133738309   .   A   G   .   .   .
chr9    133738325   .   T   C   .   .   .
chr9    133738330   .   A   G   .   .   .
chr9    133738340   .   A   G   .   .   .
chr9    133738342   .   C   G   .   .   .
ADD COMMENTlink written 8 months ago by Pierre Lindenbaum134k
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