Annotating file using bcftools

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

annotation plink bcftools

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written 2.2 years ago by kl •

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written 2.2 years ago by Pierre Lindenbaum

1 answer

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

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written 2.2 years ago by Pierre Lindenbaum

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

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written 2.2 years ago by 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

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updated 2.2 years ago by Pierre Lindenbaum

• written 2.2 years ago by 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.

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written 2.2 years ago by kl •