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  • vcftools --max-alleles default?

    I have been filtering some gbs data as follows:

    vcftools --vcf chr1.vcf --minDP 5 --minGQ 98 --maf 0.01 --hwe 0.05 --max-missing 0.2 --recode

    I am not filtering out multi-allelic (>2) sites yet. Still, I get the following:

    Parameters as interpreted:
    --vcf c1.ang.vcf
    --maf 0.01
    --max-alleles 2
    --minDP 5
    --minGQ 98
    --hwe 0.05
    --max-missing 0.2
    --out filtered/c1.ang.filt.vcf
    --recode

    Is the --max-alleles filter set by default to 2?

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