bcftools=1.18 not filtering correcting MAF
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12 weeks ago
AMARU • 0

Hi, I have encountered some issues when using bcftools v.1.11, v.1.14 or v.1.18

I want to filter MAF<=0.01 & 'F_MISSING<0.1' for rare-variant analysis. I have a vcf file mapped to the GRCh37, left aligned, and multi-allelic split.

bcftools view -q 0.01:minor test1.vcf > test2.vcf --> This filter variants with MAF >=0.01, how can I filter variants with maf<=0.01?

Then I tried: bcftools filter -i 'MAF<0.01' test1.vcf > test2.vcf OR bcftools view -i 'MAF<=0.01' test1.vcf > test2.vcf Both cases provided me maf<=0.01 but I spotted few ones with maf>=0.01

CHROM POS AC AN
1 13012 2 506
1 13270 2 516
1 13271 2 516
1 13600 4 516
1 14792 4 516
1 14842 4 516
1 14975 2 516
1 16856 1 516
1 16869 1 516
1 16886 1 516
1 17005 5 512
1 17379 3 516
1 17556 3 516
1 17563 3 516
1 69270 346 346
1 69511 502 502
1 76838 1 226
1 83923 0 86
1 87269 2 216
1 101158 **130 130**
1 128798 48 48
1 135982 408 408
1 136122 2 484
1 136131 1 484
1 137923 1 516
1 138039 3 514
1 138343 1 516
1 138802 3 516
1 139019 1 516
1 139363 2 516
1 139393 4 516
1 139533 2 516
1 139537 1 516
1 139739 1 508
1 139838 3 500
1 139967 242 244
1 162463 1 430
1 229673 114 114
1 234336 3 496
1 324795 2 394
1 324883 3 388
1 324890 2 386
1 324894 2 386
1 324895 2 386
1 569337 4 450
1 658478 1 490
1 664430 1 516
1 664496 2 516
1 664568 5 516
1 664608 1 516
1 665044 1 516
1 665058 5 516
1 665108 1 516
1 668476 1 516
1 668582 1 516
1 668605 2 516
1 668677 3 514
1 668810 2 450
1 672048 1 516
1 712705 16 16
1 715140 0 142
1 715140 6 6
1 715142 0 142
1 715348 164 164
1 715996 114 114
1 717421 4 476
1 721667 3 516
1 726481 170 170
1 731181 1 182
1 731256 1 320
1 731265 1 332
1 739426 64 64
1 741244 3 510
1 753269 74 74
1 755887 112 112
1 758141 0 80
1 758144 80 80
1 758324 92 92
1 761930 2 506
1 762307 5 516
1 762566 2 512
1 767780 130 130
1 769829 106 106
1 770075 36 36
1 771410 32 32
1 777232 5 504
1 777348 3 516
1 777449 5 516
1 777690 1 516
1 780027 96 96
1 782982 1 516
1 783071 1 516
1 783149 2 516
1 783304 158 158
1 789256 66 66
1 792144 1 462
1 792478 3 516
1 792480 **516 516**
1 799463 92 92
1 807761 18 18

Any ideas would be highly appreciated!

bcftools minor-allele-frequency VCF • 384 views
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Hello, Is MAF flag defined in your VCF?

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No, it is not. I thought that those arguments were enough. How can I flag MAF in the bcftools?

I spotted a similar thing in plink2.

Thanks

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