[Vcftools-help] trouble filtering vcf file for minor allele frequency

[Rabail Z. <rab...@gm...>]

Hi,

Ive downloaded vcf files from 1000 genomes and the INFO column is reordered
like in the screenshot attached.

command:

*tabix -h
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr20.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz
<ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr20.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz>
20:6767838-7367838  -c NA18525 -c NA18526 -c NA18528.....*

However, when i manually download the file from browser, the INFO column is
like:

AA=T|||;AC=78;AF=0.0163738;AFR_AF=0.059;AMR_AF=0.0058;AN=1322;DP=101591;EAS_AF=0;EUR_AF=0;NS=2504;SAS_AF=0;SF=0,1,2,3,4,5,6;VT=SNP

when i apply a command for these two differently patterned files for minor
allele frequency cutoff 0.05, the number of SNPs resulting are not the same.

command:
*vcftools --vcf input.vcf --recode --recode-INFO-all --maf 0.05 --out
output.vcf*

it is 2136 for the screenshot file and 1757 for the manually downloaded
file.

1757 is the correct number though as it is also resulting with the
vcf_to_ped converter script over 1000 genomes for the same frequency cutoff.

What is possibly wrong? I cannot manually download all the files.

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