Question: Change ALT field in VCF
gravatar for sonia.olaechea
16 months ago by
sonia.olaechea120 wrote:

Hi all,

I have 2 vcf files for the same positions but with different individuals which I would like to merge. However, in one of the files some of my variants have a . in the ALT field, which I would like to replace by the corresponding allele. I've tried to obtain those alternatives alleles from my other vcf which looks apparently correct. I'm using the following command of vcftools:

plink --vcf my.vcf --const-fid 0 --a1-allele ALT.txt 5 3 '#' --recode --out myfile.mod.vcf

ALT.txt contains two columns: SNPID and ALTfield of my other vcf file (I've tried both with and without header). Still, the program says: Error: Fewer tokens than expected on line 1 of --a1-allele file.

I don't know what I'm doing wrong so I would appreciate it if anyone sees something that I'm not seeing or if anyone recommends other tools. Thank you very much in advanced :)

snps gwas vcf • 593 views
ADD COMMENTlink written 16 months ago by sonia.olaechea120

what is the output of

 head ALT.txt


file ALT.txt
ADD REPLYlink written 16 months ago by Pierre Lindenbaum128k
head ALT.txt 
rs10032042      G
rs10174691      C
rs10221923      G
rs10223644      G
rs1028771       C
rs10305678      G
rs10404081      G
rs10421281      C
rs1042478       G
rs10459252      C`

file ALT.txt 
file ALT.txt: ASCII text`
ADD REPLYlink modified 16 months ago • written 16 months ago by sonia.olaechea120
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