This linux command will output column 1,2, and 3 of your file into csv. Change the 1,2,3 according to the column (1-based) you want to extract. You can extract as many columns as you want.
cut -f 1,2,3 fileName.vcf | sed 's/[\t]/,/g' > cols.csv
I tried with the command but not sure why i m getting it wrong..!!
cut -f 2,6,9 file.vcf | sed 's/[\t]/,/g' > out.csv
sed: -e expression #1, char 1: unknown command: `\ufffd'
sed: -e expression #1, char 1: unknown command: `\ufffd'
By the way what else can I do for INFO column (column 9) if I want to get just DP from a list of things in that column 9 (INFO column contains e,g. AN=2;DP=87;Dels=0.00..)
vcf-subset -c POS,QUAL my.vcf.gz | tr "\t" "," > out.csv
Its giving me just the header line of the two columns in the VCF file POS and QUAL
#CHROM,POS,ID,REF,ALT,QUAL,FILTER,INFO,FORMAT,POS,QUAL
by the way I don't want any other info except the data in the columns with header
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You may want to specify if you're trying to extract 2 or more samples or simply arbitrary columns. It looks like matted's answer applies to the former, and Dk and Rm's apply to the latter.