Closed nirav572 closed 8 months ago
Adding something to the thread. It seems that -q 0.01:minor, excludes <=0.01 based on minor allele. the MAF<=0.01 seems to be doing something similar but in my case it doesnt exclude all MAF<=0.01,using bcftools/1.14 (conda env).
bcftools 1.18 seems to be the same, i mean: bcftools filter -i 'MAF<=0.01' test.vcf > test1.vcf bcftools query -f '%CHROM %POS %REF %ALT %AC %AN\n' vcf 1 13012 G A 2 506 1 13270 C T 2 516 1 13271 C T 2 516 1 13600 G T 4 516 1 14792 G A 4 516 1 14842 G A 4 516 1 14975 C T 2 516 1 16856 A G 1 516 1 16869 C T 1 516 1 16886 A G 1 516 1 17005 A G 5 512 1 17379 G A 3 516 1 17556 C T 3 516 1 17563 G A 3 516 1 69270 A G 346 346 1 69511 A G 502 502 1 76838 T G 1 226 1 83923 A G 0 86 1 87269 C A 2 216 1 101158 T C 130 130 1 128798 C T 48 48 1 135982 A G 408 408 1 136122 G A 2 484 1 136131 C T 1 484 1 137923 C T 1 516 1 138039 T A 3 514 1 138343 G T 1 516 1 138802 T G 3 516 1 139019 G C 1 516 1 139363 T C 2 516
Both use the same underlying htslib's bcf_calc_ac()
function which sets AC,AN from existing INFO tags or, when absent, from GT fields. They should give the same results.
Hi, what's the difference between the two approaches to filter for variants above a certain MAF threshold?
bcftools view -q 0.01
v/sbcftools -i 'MAF>0.01'
? Also, do they compute the MAF value, or look for it in tag info?Thank you!