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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