Error while using VCFtools (--maf) to filter by allele frequency

Question

[kshaffman]

I am trying to filter my VCF file by allele frequency. I am trying to figure out how to do this using VCF tools --maf.

My input was as follows:

-vcf "/u/home/k/kshaffma/dir/parents_uniq_with_annotations.vcf" --recode --maf 0.1 --out "/u/home/k/kshaffma/dir/parents_uniq_with_annotations_alelle_freq_greater_than_0.1.vcf"

Here was the error I got:

Warning: Expected at least 2 parts in INFO entry: ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
Warning: Expected at least 2 parts in INFO entry: ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
Warning: Expected at least 2 parts in FORMAT entry: ID=SnpSift,Description="SnpSift 4.3t (build 2017-11-24 10:18), by Pablo Cingolani, Expression used: ( EFF[*].IMPACT = 'LOW')">
After filtering, kept 0 out of 0 Individuals
Outputting VCF file...
Error: Require Genotypes in variant file to filter by frequency and/or call rate

Does anyone know what this error means and how I can fix it? My VCF files are annotated, could that potentially be the issue.

ALSO

I tried to use bcftools view -q but I can't figure out what the input would be to get the desired filtering.

What the program says is the following:

-q/Q, --min-af/--max-af <float>[:<type>]    minimum/maximum frequency for non-reference (nref), 1st alternate (alt1), least frequent
                                               (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles [nref]

I know that my command needs to be something like:

bcftools view -q [minor 0.1] 'file'

But I don't know the exact syntax. If someone would be willing to help me with either of these two problems I would really appreciate it.

Answer 1

[Giacomo Rocchetti]

Apparently your vcf file is missing the genotypes. There are already some older threads addressing this issue:

• vcftools Error: Require Genotypes in VCF file in order to output as 0/1/2 matrix.
• VCFTOOLS error while trying to filter for MAF