verifybamid results with freemix < 2% and chipmix > 10%

Question

[GK1610]

I ran verifyBAMID on each 200 chip-seq BAM files with input merged vcf file of Genotypes of 600 samples ( 200 of them are chip-seq individuals). I had AF,AC,AN in the info column which was calculated using these genotypes.

~80% of 200 samples are Caucasians.

I am struggling to decide for the samples which have freemix < 2% but chipmix >2%

for sample 1365, I had histone modified chip-seq sample 1365_A with two input samples 1365_Pos_IN_2, 1365_Pos_IN_1.

histone modified chip-seq BAM 1365_A has .00669 whereas chipmix is 0.3765 where with input samples it does resonable job with correct matching of genotype column and reasonable chipmix and freemix values. Why chipmix is so high for histone sample

SEQ_ID RG CHIP_ID #SNPS #READS AVG_DP FREEMIX FREELK1 FREELK0 FREE_RH FREE_RA CHIPMIX CHIPLK1 CHIPLK0 CHIP_RH CHIP_RA DPREF RDPHET RDPALT
1365_A ALL 1365_A 683278 436495 0.64 0.00669 160631.69 160867.97 NA NA 0.37645 145839.46 194576.92 NA NA 0.657 0.9478 0.9369
1365_Pos_IN_2 ALL 1365_A 683278 1770725 2.59 0.00320 676736.66 676773.49 NA NA 0.00298 425582.72 426459.54 NA NA 2.598 0.9965 0.9923
1365_Pos_IN_1 ALL 1365_A 683278 1127574 1.65 0.00000 446421.43 446421.43 NA NA 0.00193 254020.46 254353.15 NA NA 1.653 0.9961 0.9982

What does it mean when your target sample matched with the intended sample genotype from vcf file with < 2% free mix value but with chipmix value > 2% for sample 1368_A and 1213_A

1368_A ALL 1368_A 683278 450800 0.66 0.01019 167252.18 167673.56 NA NA 0.56004 158591.79 248605.77 NA NA 0.677 0.9507 0.9477
1213_A ALL 1213_A 683278 945562 1.38 0.01361 345881.30 347208.39 NA NA 0.97533 346470.85 647079.17 NA NA 1.396 0.9783 0.9891

This is clearly contaminated sample with 1287_A. then why its chipmix is not 0.9?

1215_Pos_IN ALL 1287_A 683278 3336277 4.88 0.15412 1360018.71 1407231.58 NA NA 0.18590 1109098.83 1431053.16 NA NA 4.900 0.9941 0.9917

[WouterDeCoster]

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[GK1610]

Thanks, this is helpful.