how to remove positions in VCF based on rsID

hi all,

I am trying to remove entries in the VCF file based on rs_id. I tried to use bcftools view but for some reason preparing a list of the positions I need to be excluded did not work.

A sample of the file looked like this:

22 rs165886
22 rs165608
22 rs1541529
22 rs4819925
22 rs5992604

and the bcftools command is the following:

bcftools view -T ^tlist.txt input.vcf

which always give an error Could not parse the file

so I tried to change the value in the plink map file to -1 like the below, and then I recoded it again using plink to vcf. even after all of that, the positions are still in the vcf file.

22  rs165886    -1  17339003
22  rs165608    -1  17339404

Can you please tell me how to fix this?

vcf plink bcftools

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updated 3.1 years ago by Ram

• written 4.5 years ago by raalsuwaidi •

Do an inverse grep

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written 4.5 years ago by cpad0112

You mean an inverse grep on the VCF file? I am no expert in that, can you please give me an example? Will it remove the whole line?

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written 4.5 years ago by raalsuwaidi •

with example vcf and example file with one rsid:

$ cat test.vcf 
##fileformat=VCFv4.1
##filedate=2017.7.5
##source=Minimac3
##contig=<ID=29>
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=DS,Number=1,Type=Float,Description="Estimated Alternate Allele Dosage : [P(0/1)+2*P(1/1)]">
##INFO=<ID=AF,Number=1,Type=Float,Description="Estimated Alternate Allele Frequency">
##INFO=<ID=MAF,Number=1,Type=Float,Description="Estimated Minor Allele Frequency">
##INFO=<ID=R2,Number=1,Type=Float,Description="Estimated Imputation Accuracy">
##INFO=<ID=ER2,Number=1,Type=Float,Description="Empirical (Leave-One-Out) R-square (available only for genotyped variants)">
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  1242658141  1364665948  1242658615
10  96633300    rs4919045   G   A   .   PASS    .   GT:DS   0|0:0.193   0|0:0.193   0|0:0.193
29  11  Chr29:11    A   G   .   PASS    .   GT:DS   0|0:0.193   0|0:0.193   0|0:0.193

$ cat test.txt 
rs4919045

$ grep -vf test.txt test.vcf

##fileformat=VCFv4.1
##filedate=2017.7.5
##source=Minimac3
##contig=<ID=29>
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=DS,Number=1,Type=Float,Description="Estimated Alternate Allele Dosage : [P(0/1)+2*P(1/1)]">
##INFO=<ID=AF,Number=1,Type=Float,Description="Estimated Alternate Allele Frequency">
##INFO=<ID=MAF,Number=1,Type=Float,Description="Estimated Minor Allele Frequency">
##INFO=<ID=R2,Number=1,Type=Float,Description="Estimated Imputation Accuracy">
##INFO=<ID=ER2,Number=1,Type=Float,Description="Empirical (Leave-One-Out) R-square (available only for genotyped variants)">
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  1242658141  1364665948  1242658615
29  11  Chr29:11    A   G   .   PASS    .   GT:DS   0|0:0.193   0|0:0.193   0|0:0.193

If vcf is gzipped, you can use zgrep instead of regular grep.

You can also try this and I haven't tested it's performance:

$ awk -F "\t" 'FNR==NR{a[$1]++;next}!a[$3]' test.txt test.vcf

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written 4.5 years ago by cpad0112

grep -vFwf test.txt test.vcf

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written 4.5 years ago by Pierre Lindenbaum

Thanks. That worked

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written 4.5 years ago by raalsuwaidi •

1 answer

bcftools view -e 'ID=@list_of_rs_id.txt'  in.vcf

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written 4.5 years ago by Pierre Lindenbaum