Annotating file using bcftools

Question

[kl]

Hi all,

I am trying to annotate my imputed genetic file using bcftools and then want to convert it to plink.

bcftools index -t ro_imputed_hrcgrch37.R2_0.3.vcf.gz
bcftools annotate \
-a $DATADIR/ro_imputed_hrcgrch37.R2_0.3.vcf.gz \
-c ID $REF/All_20180423.vcf.gz \
--output-type z \
-o $DATADIR/ro_imputed_hrcgrch37.R2_0.3.vcf_dbSNP151.vcf.gz

This seems to work but my samples are removed. Consequently, when I try to convert to binary plink files, it doesn't work because it says I have no samples. Can anyone give advice on what I've done wrong?

Many thanks

[Pierre Lindenbaum]

Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they all work. If an answer was not really helpful or did not work, provide detailed feedback so others know not to use that answer.

• Annotating file using bcftools
• Post-imputation plot
• Genetic data QC prior to imputation
• Repeated measures in GWAS and polygenic risk scores analyses
• How to perform GWAS using BOLT-LMM iteratively for many phenotypes in bash
• Post-imputation steps (cleaning and converting to plink)
• Do you always need to clump polygenic risk scores?
• Check whether two GWAS are from the same ancestry
• How to convert a meta-analysis file from PLINK (.meta) to a .csv or.txt to be read into R?

Answer 1

[Pierre Lindenbaum]

I think your're annotating $REF/All_20180423.vcf.gz (DBSNP isn't it ? = no genotype) with your vcf as the database ro_imputed_hrcgrch37.R2_0.3.vcf.gz but your want the reverse : annotate your vcf with dbsnp.

bcftools annotate \
-a $REF/All_20180423.vcf.gz  \
-c ID $DATADIR/ro_imputed_hrcgrch37.R2_0.3.vcf.gz \
--output-type z \
-o $DATADIR/ro_imputed_hrcgrch37.R2_0.3.vcf_dbSNP151.vcf.gz

[kl]

Thanks - I corrected it. It doesn't seem to annotate. I converted to binary after which is what is shown below. It is not the output I want. The second column I wanted to be the rsid extracted from the All_2018423.vcf.gz file. based on chromosome, position and allele match. I would appreciate any suggestions. I haven't used bcftools before.

22 22:51218224:C:A 0 51218224 A C 22 22:51218377:G:C 0 51218377 C G 22 22:51219006:G:A 0 51219006 A G 22 22:51219387:T:C 0 51219387 C T 22 22:51221190:G:A 0 51221190 A G 22 22:51221731:T:C 0 51221731 C T 22 22:51222100:G:T 0 51222100 T G 22 22:51223637:G:A 0 51223637 A G 22 22:51229805:T:C 0 51229805 C T 22 22:51237063:T:C 0 51237063 C T

Thanks

[kl]

It worked with this bcftools index -t $DATADIR/cpro_imputed_hrcgrch37.R2_0.3.vcf.gz

bcftools annotate  \
-a $RefGenomes/All_20180423.vcf.gz  \
-c CHROM,FROM,TO,ID $DATADIR/ro_imputed_hrcgrch37.R2_0.3.vcf.gz \
-output-type z \
-o $DATADIR/ro_imputed_hrcgrch37.R2_0.3.vcf_dbSNP151.vcf.gz

[kl]

Do you know if there is a way to leave chr:pos in ID if there is no matching rsid based on chromosome and position, as variants have been reduced by half.