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I have an excel file that I created from VCF file for common SNPs across 6 samples. This excel have the chromosomes and the position of the SNPs only (see example table1) enter image description here Now I would like to obtain the other information (eg. allels, Genotype, depth, etc) from the VCF files of the 6 samples (i.e. the one that contains these positions). I tried using AWK command like here for position 23432 on chr. 1 for the 6 file :

awk -F " " '$1=="1" && $2=="23432"' file1.vcf
awk -F " " '$1=="1" && $2=="23432"' file2.vcf
awk -F " " '$1=="1" && $2=="23432"' file3.vcf
awk -F " " '$1=="1" && $2=="23432"' file4.vcf
awk -F " " '$1=="1" && $2=="23432"' file5.vcf
awk -F " " '$1=="1" && $2=="23432"' file6.vcf

he issue is that these SNPs I have are thousands positions, so I need an automated way to do this

Could you advise on that ?

Thanks

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  • $\begingroup$ Is this related to your previous question? Is this the sites file that you opened using Excel? Please read the bcftools manual, they have everything you need. $\endgroup$
    – Ram RS
    May 24 at 17:52
  • $\begingroup$ When working with VCF files, a tab-separated format, you want -F '\t'. And you never want -F " ", unless you truly want to break on spaces and only spaces. By default awk will split on any whitespace character (including tabs and spaces) so you don't need this. $\endgroup$
    – terdon
    May 24 at 18:04
  • $\begingroup$ Don’t use awk or excel, please just use bcftools and save yourself a lot of trouble $\endgroup$
    – user438383
    May 24 at 19:44
  • $\begingroup$ @user438383 OP has a separate thread going on with bcftools involved in solving this problem, looks like they chose to open a new thread for no apparent reason. $\endgroup$
    – Ram RS
    May 24 at 21:03

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