This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to convert genomic region of following type to vcf file?

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?

vcf conversion liftover
• 1,086 views • link
updated by Pierre Lindenbaum Pierre Lindenbaum • written by svp svp

1 answer 

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   .   .   .
• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Log in to answer this question.

More posts like this