bcftools reheader -h

Question

[marta.rusmini]

Hi sorry for the very basic question! I would like to change the tags of the INFO fields of my vcf. I saw the bcftools -reader option but I cannot understand the format of the newheader.vcf that I need. Can anyone help me? I will appreciate help in order to a)create the new file needed for the script b)write the script (is it correct

bcftools reheader -h newheader.vcf filetochange.vcf

?

here an example of part of a header that I want to modify (i would like to change the ID=xxx)

##INFO=<ID=dbNSFP_ExAC_NFE_AF,Number=A,Type=Float,Description="Field 'ExAC_NFE_AF' from dbNSFP">
##INFO=<ID=dbNSFP_ExAC_SAS_AF,Number=A,Type=Float,Description="Field 'ExAC_SAS_AF' from dbNSFP">
##INFO=<ID=dbNSFP_GERP___RS,Number=A,Type=Float,Description="Field 'GERP++_RS' from dbNSFP">
##INFO=<ID=dbNSFP_GERP___NR,Number=A,Type=Float,Description="Field 'GERP++_NR' from dbNSFP">
##INFO=<ID=dbNSFP_ExAC_Adj_AC,Number=A,Type=Integer,Description="Field 'ExAC_Adj_AC' from dbNSFP">
##INFO=<ID=dbNSFP_ExAC_Adj_AF,Number=A,Type=Float,Description="Field 'ExAC_Adj_AF' from dbNSFP">
##INFO=<ID=dbNSFP_ExAC_SAS_AC,Number=A,Type=Integer,Description="Field 'ExAC_SAS_AC' from dbNSFP">
##INFO=<ID=dbNSFP_1000Gp3_AMR_AF,Number=A,Type=Float,Description="Field '1000Gp3_AMR_AF' from dbNSFP">
##INFO=<ID=dbNSFP_1000Gp3_AMR_AC,Number=A,Type=Integer,Description="Field '1000Gp3_AMR_AC' from dbNSFP">
##INFO=<ID=dbNSFP_MetaSVM_pred,Number=A,Type=Character,Description="Field 'MetaSVM_pred' from dbNSFP">
##INFO=<ID=dbNSFP_1000Gp3_EAS_AC,Number=A,Type=Integer,Description="Field '1000Gp3_EAS_AC' from dbNSFP">

thank you!

[whitneyt]

Hello!

I have come across this thread and am wondering if I open my VCF file as a text file, can I edit the header manually?

I need to remove the

##contig=<ID=0,length=2147483645>

and change :

##contig=<ID=24,length=28817459>
##contig=<ID=25,length=155234708>
##contig=<ID=26,length=16391>

to

##contig=<ID=X,length=28817459>
##contig=<ID=Y,length=155234708>
##contig=<ID=MT,length=16391>

Can I do this in the text editor window and then resave file as a new .vcf? Instead of using bcftools?

thank you!!

[hiruna72]

try bcftools reheader -f option .fai file option to change contig names and lengths

$ bcftools reheader -f XXX.fasta.fai old.vcf -o new.vcf

Answer 1

[finswimmer]

bcftools reheader is for replacing the complete header of your vcf file. If this ist what you want to do, create a text file with the new header as the content, e.g. header.hr:

##fileformat=VCFv4.1
##INFO=<ID=CSQ,Number=.,Type=String,Description="some text">
##INFO=<ID=NEW,Number=.,Type=String,Description="some text">
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO

As you can see you also need to define the columns!

Than you can replace the old header with the new one with:

$ bcftools reheader -h header.hr input.vcf > output.vcf

Answer 2

[Pierre Lindenbaum]

bcftools annotate https://samtools.github.io/bcftools/bcftools.html

-c, --columns list

The imported VCF annotations can be renamed as "DST_TAG:=SRC_TAG" or "FMT/DST_TAG:=FMT/SRC_TAG".