Why IBD is very high for self and best matching individual ?

[gatla]

Hi,

I am not from genetics background.

I am a bit confused about high IBD for self and best matching individual. I was thinking that if there is a sample swap, the IBD will be very high for the swapped sample but in my case, I have very high IBD for self and best matching individual, Could some explain if this is expected ?

From the bestSM and bestRG, it looks like the samples were swapped.

verbose
Best Matching Individual is sample_894 with IBD = 0.994098
Self Individual is sample_835 with IBD = 0.996443

selfSM
#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
sample_835    ALL    sample_835    182562    3380281    18.52    0.00626    840385.57    845277.10    NA    NA    0.99644    842608.65    1051188.19    NA    NA    19.574    0.8776    0.9465


selfRG
#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
sample_835    sample_835    sample_894    182562    3380281    18.52    0.00626    840385.57    845277.10    NA    NA    0.99644    842608.651051188.19    NA    NA    19.574    0.8776    0.9465

bestSM
#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
sample_835    ALL    sample_894    182562    3380281    18.52    0.00626    840385.57    845277.10    NA    NA    0.00590    785762.39    790812.57NA    NA    19.221    0.9337    0.9504

bestRG
#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
sample_835    sample_835    sample_894    182562    3380281    18.52    0.00626    840385.57    845277.10    NA    NA    0.00590    785762.39790812.57    NA    NA    19.221    0.9337    0.9504

[Hyun Min Kang]

What does the verbose output say for other individuals?

Hyun.

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[gatla]

Comparing with other individuals:

Self Individual is sample_835

Comparing with individual sample_883.. Optimal fIBD = 0.003940, LLK0 = 1121274.183459, LLK1 = 897778.924333 for readgroup -1
Comparing with individual sample_894.. Optimal fIBD = 0.993427, LLK0 = 844598.515308, LLK1 = 838612.247422 for readgroup -1
Comparing with individual sample_905.. Optimal fIBD = 0.003864, LLK0 = 1124151.517843, LLK1 = 897760.773441 for readgroup -1
Comparing with individual sample_916.. Optimal fIBD = 0.003808, LLK0 = 1124971.846429, LLK1 = 897765.105662 for readgroup -1
Comparing with individual sample_927.. Optimal fIBD = 0.003879, LLK0 = 1121712.409593, LLK1 = 897693.570482 for readgroup -1
Comparing with individual sample_938.. Optimal fIBD = 0.003923, LLK0 = 1120562.634480, LLK1 = 897895.241345 for readgroup -1
Comparing with individual sample_832.. Optimal fIBD = 0.003890, LLK0 = 1119772.093021, LLK1 = 897730.002425 for readgroup -1
Comparing with individual sample_843.. Optimal fIBD = 0.003879, LLK0 = 1122309.886196, LLK1 = 897696.928429 for readgroup -1
Comparing with individual sample_853.. Optimal fIBD = 0.003771, LLK0 = 1122883.618506, LLK1 = 897762.130302 for readgroup -1
Comparing with individual sample_854.. Optimal fIBD = 0.003907, LLK0 = 1119644.516565, LLK1 = 897716.246822 for readgroup -1
Comparing with individual sample_855.. Optimal fIBD = 0.003954, LLK0 = 1123655.963514, LLK1 = 897560.916835 for readgroup -1
Comparing with individual sample_856.. Optimal fIBD = 0.003914, LLK0 = 1124100.892591, LLK1 = 897798.249066 for readgroup -1
Comparing with individual sample_857.. Optimal fIBD = 0.003822, LLK0 = 1126327.196762, LLK1 = 897712.980500 for readgroup -1
Comparing with individual sample_858.. Optimal fIBD = 0.003828, LLK0 = 1122612.098542, LLK1 = 897803.872394 for readgroup -1
Comparing with individual sample_859.. Optimal fIBD = 0.003823, LLK0 = 1121515.487624, LLK1 = 897771.410291 for readgroup -1
Comparing with individual sample_860.. Optimal fIBD = 0.003943, LLK0 = 1120867.046365, LLK1 = 897700.535823 for readgroup -1
Comparing with individual sample_862.. Optimal fIBD = 0.003923, LLK0 = 1123326.717983, LLK1 = 897642.099326 for readgroup -1
Comparing with individual sample_863.. Optimal fIBD = 0.003809, LLK0 = 1123211.777210, LLK1 = 897791.451265 for readgroup -1
Comparing with individual sample_864.. Optimal fIBD = 0.003910, LLK0 = 1120852.161496, LLK1 = 897645.776633 for readgroup -1
Comparing with individual sample_865.. Optimal fIBD = 0.003862, LLK0 = 1117791.806157, LLK1 = 897647.310325 for readgroup -1
Comparing with individual sample_866.. Optimal fIBD = 0.003932, LLK0 = 1120903.744927, LLK1 = 897648.905619 for readgroup -1
Comparing with individual sample_831.. Optimal fIBD = 0.003867, LLK0 = 1123105.175279, LLK1 = 897799.005738 for readgroup -1
Comparing with individual sample_867.. Optimal fIBD = 0.003988, LLK0 = 1119091.214637, LLK1 = 897731.099228 for readgroup -1
Comparing with individual sample_868.. Optimal fIBD = 0.004005, LLK0 = 1124576.086987, LLK1 = 897440.028209 for readgroup -1
Comparing with individual sample_834.. Optimal fIBD = 0.003772, LLK0 = 1121529.232756, LLK1 = 897796.142176 for readgroup 0
Comparing with individual sample_835.. Optimal fIBD = 0.004000, LLK0 = 1118467.806564, LLK1 = 897782.358322 for readgroup -1

[Hyun Min Kang]

I think this is clearly a sample swap

[gatla]

Thanks for the promopt reply. I am almost certain its a mislabeling problem. I am a bit confused with fIBD and IBD. The log file at the end says:

Best Matching Individual is sample_894 with IBD = 0.993427
Self Individual issample_835 with IBD = 0.996000

The fIBD with self is 0.004 and self IBD is 0.996. Whats the difference between fIBD and IBD ?

[Hyun Min Kang]

fIBD is 1-CHIPMIX. I think the labeling is consistent.

Hyun.

[gatla]

Sorry, I did not get it "labeling is consistent". Do you mean its not a sample swap ?

[Hyun Min Kang]

I meant that the labeling of CHIPMIX and fIBD, etc are consistent (from the software perspective, not the results).

Hyun.

[gatla]

Thank you very much for taking time and clarifying it,