bcftools merge heterozygous calls

Question

[evelyn]

Hello,

I have merged three vcf files and translated the SNP calls using bcftools query and awk. I want to change the heterozygous calls as IUPAC codes:

Code Base
R   A or G
Y   C or T
S   G or C
W   A or T
K   G or T
M   A or C
N   any base

I tried using:

bcftools query -f '%CHROM\t%POS\t%ID\t%REF\t%ALT[\t%TGT]\n' merge.vcf | awk -v FS="\t" -v OFS="\t" '{for(i=6;i<=NF;i++) {split($i, gt, "/"); if(gt[1]==".") $i="NA"; else if(gt[1]==gt[2]) $i=gt[1]; else if(gt[2]=="A" || gt[2]=="G") $i="R";  else if(gt[2]=="C" || gt[2]=="T") $i="Y"; else if(gt[2]=="G" || gt[2]=="C") $i="S"; else if(gt[2]=="A" || gt[2]=="T") $i="W"; else if(gt[2]=="G" || gt[2]=="T") $i="K"; else if(gt[2]=="A" || gt[2]=="C") $i="M"; else $i="N";} print }' > out.vcf

But it gives wrong IUPAC codes:

CHROM POS ID REF ALT File1 File2 File3
1   441 .   G   T   T   Y   NA
1   447 .   G   A   A   R   NA
1   452 .   G   A   A   A   NA
1   468 .   G   T   T   Y   NA
1   473 .   T   C   C   C   NA
1   474 .   G   T   T   Y   NA
1   489 .   T   A   A   A   NA
1   555 .   A   G   G   G   NA
1   577 .   T   G   G   G   NA
1   578 .   A   T   T   T   NA
1   909 .   C   A   A   NA  NA

But it gives wrong IUPAC codes for example, for G or T (pos 468 for File 2), it should give a K but gives Y. I think I am missing something in the command here. Thank you for your help!

Answer 1

[finswimmer]

Hello evelyn ,

why have you deleted your original post (I have reopened it) and moved your comment to a new question? It is absolutely fine to stay in the old thread so others can see the context of your question.

if(gt[2]=="A" || gt[2]=="G") $i="R";

That's not correct. It is R for the genotypes AG or GA and not if the second value is A or G.

if((gt[1]=="A" && gt[2]=="G") || (gt[1]=="G" && gt[2]=="A")) $i="R";

Same for the other combinations.

Or instead of comparing the splitted values use the complete field value:

if($i == "A/G" || $i == "G/A") $i="R";

or even shorter using regex:

if($i ~ /(A\/G) || (G\/A)/) $i="R";

fin swimmer

[evelyn]

Thank you, @fin swimmer! It worked perfectly. I accidentally deleted my post and I did not know how to recover it :/ Thank you!

[evelyn]

The above command converted A\G or G\A to R as:

bcftools query -f '%CHROM\t%POS\t%ID\t%REF\t%ALT[\t%TGT]\n' merge.vcf | awk -v FS="\t" -v OFS="\t" '{for(i=6;i<=NF;i++) {split($i, gt, "/"); if(gt[1]==".") $i="NA"; else if (gt[1]==gt[2]) $i=gt[1]; else if($i ~ /(A\/G) || (G\/A)/) $i="R";  else if($i ~ /(C\/T) || (T\/C)/) $i="Y"; else if($i ~ /(G\/C) || (C\/G)/) $i="S"; else if($i ~ /(A\/T) || (T\/A)/) $i="W"; else if($i ~ /(G\/T) || (T\/G)/) $i="K"; else if($i ~ /(A\/C) || (C\/A)/) $i="M"; else $i="N";} print }' > out.vcf

But it converts all the heterozygous calls to R only. There is no error and the file is produced but only to R. I am not sure what is missing.