How to add FORMAT/TAG = "." to all samples in a vcf file via bcftools?

Question

[Марта]

Hello, all. I'm trying to add FORMAT/TAG annotation to all samples in my vcf file and I want it to be a missing value (".") or 0 for all of them. Is there a way to do this with bcftools?

Answer 1

[Pierre Lindenbaum]

using vcffilterjdk https://jvarkit.readthedocs.io/en/latest/VcfFilterJdk/

bcftools view in.vcf.gz |\
awk '/^#CHROM/ {printf("##FORMAT=<ID=TAG,Number=1,Type=Integer,Description=\"x\">\n");} {print}' |\
java -jar ${JVARKIT_DIST}/jvarkit.jar vcffilterjdk -e 'return new VariantContextBuilder(variant).genotypes(variant.getGenotypes().stream().map(G->new GenotypeBuilder(G).attribute("TAG",0).make()).collect(Collectors.toList())).make();'

[Марта]

Thank you for the answer! This works, although I noticed that if add a second TAG to the edited vcf with the same method it replaces the first one I added. Could you help me figure out how to add more than one TAG?

[Pierre Lindenbaum]

Could you help me figure out how to add more than one TAG?

run the script twice by changing the name "TAG" to "TAG2" ...

[Марта]

I did, I ran

bcftools view in.vcf.gz |\
awk '/^#CHROM/ {printf("##FORMAT=<ID=TAG1,Number=1,Type=Integer,Description=\"x\">\n");} {print}' |\
java -jar jvarkit.jar vcffilterjdk -e 'return new VariantContextBuilder(variant).genotypes( variant.getGenotypes().stream().map(G->new GenotypeBuilder(G).attribute("TAG1",0).make()).collect(Collectors.toList()) ).make();' > out1.vcf

and then

bcftools view out1.vcf.gz |\
awk '/^#CHROM/ {printf("##FORMAT=<ID=TAG2,Number=1,Type=Integer,Description=\"x\">\n");} {print}' |\
java -jar jvarkit.jar vcffilterjdk -e 'return new VariantContextBuilder(variant).genotypes( variant.getGenotypes().stream().map(G->new GenotypeBuilder(G).attribute("TAG2",0).make()).collect(Collectors.toList()) ).make();' > out2.vcf

In the resulting out2.vcf, both ##FORMAT=<ID=TAG1..> and ##FORMAT=<ID=TAG2..> are present, but all of the samples only have TAG2 in their FORMAT fields. I'm not familiar with Java so I'm not sure what can be done to correct this. Could you help please?

[Pierre Lindenbaum]

works on my machine:

 gunzip -c in.vcf.gz | awk '/^#CHROM/ {printf("##FORMAT=<ID=TAG1,Number=1,Type=Integer,Description=\"x\">\n");printf("##FORMAT=<ID=TAG2,Number=1,Type=Integer,Description=\"x\">\n");} {print}' | java -jar jvarkit.jar vcffilterjdk -e 'return new VariantContextBuilder(variant).genotypes( variant.getGenotypes().stream().map(G->new GenotypeBuilder(G).attribute("TAG1",0).make()).collect(Collectors.toList()) ).make();' | java -jar jvarkit.jar vcffilterjdk -e 'return new VariantContextBuilder(variant).genotypes( variant.getGenotypes().stream().map(G->new GenotypeBuilder(G).attribute("TAG2",0).make()).collect(Collectors.toList()) ).make();'  | grep -v "##" | cut -f 9- | head

FORMAT  S1  S2  S3  S4  S5
GT:PL:TAG1:TAG2 0/0:0,9,47:0:0  0/0:0,18,73:0:0 0/0:0,18,73:0:0 0/0:0,33,116:0:0    1/1:95,24,0:0:0
GT:PL:TAG1:TAG2 0/0:0,15,57:0:0 0/1:31,0,5:0:0  0/1:31,0,5:0:0  0/0:0,9,42:0:0  0/0:0,24,69:0:0
GT:PL:TAG1:TAG2 0/0:0,33,122:0:0    0/0:0,39,135:0:0    0/0:0,39,135:0:0    1/1:100,30,0:0:0    0/0:0,27,109:0:0
GT:PL:TAG1:TAG2 0/1:37,0,50:0:0 0/0:0,22,116:0:0    0/0:0,22,116:0:0    0/0:0,21,94:0:0 0/0:0,12,62:0:0
GT:PL:TAG1:TAG2 0/0:0,18,83:0:0 0/1:24,0,40:0:0 0/1:24,0,40:0:0 0/0:0,27,111:0:0    0/0:0,10,78:0:0
GT:PL:TAG1:TAG2 0/1:70,0,159:0:0    0/0:0,15,225:0:0    0/0:0,15,225:0:0    0/0:0,27,231:0:0    0/0:0,27,168:0:0
GT:PL:TAG1:TAG2 0/0:0,18,84:0:0 1/1:111,27,0:0:0    1/1:111,27,0:0:0    0/0:0,21,92:0:0 0/0:0,45,141:0:0
GT:PL:TAG1:TAG2 0/0:0,27,109:0:0    0/0:0,24,95:0:0 0/0:0,24,95:0:0 1/1:109,27,0:0:0    0/0:0,42,140:0:0
GT:PL:TAG1:TAG2 0/0:0,33,124:0:0    0/0:0,30,117:0:0    0/0:0,30,117:0:0    0/0:0,27,111:0:0    1/1:111,33,0:0:0