Re: Sample swap and IBD interpretation

[Hyun Min Kang]

1. I think so.

2. I guess this might be a bug, and will look into it.

3. IBD is opposite of contamination value, and I guess that's why. I do not know which output you are talking about

On Sat, Aug 25, 2018 at 7:33 AM atla goutham <goutha...@gmail.com> wrote:

Hi All,

I am posting the verifyBamID results for few of the samples I have been analysing.  I have couple of questions:

1. I understood that there is a clear mislabelling of all samples as CHIPMIX is almost 1 for all the samples. The correct labelling is given by bestRG file. Is my understanding correct ?

2. In the wiki page, its mentioned that the CHIP_ID for selfSM and selfRG should always be equal to SEQ_ID, but here I do not see that, in selfRG file, SEQ_ID is not CHIP_ID ? 

3. Why IBD is very high for both self and best matching sample in Verbose output ? 

LOGS:

selfSM:

#SEQ_ID         CHIP_ID       FREEMIX  CHIPMIX

sample_841 sample_841 0.00912 0.99553

sample_845 sample_845 0.01125 0.99451

sample_930 sample_930 0.00975 0.99459

sample_931 sample_931 0.01073 0.99449

sample_935 sample_935 0.00865 0.99606

sample_936 sample_936 0.00660 0.99708

sample_937 sample_937 0.00567 0.99744

sample_939 sample_939 0.00555 0.99747

sample_940 sample_940 0.01142 0.99432

sample_941 sample_941 0.00844 0.99617

sample_943 sample_943 0.00832 0.99613

selfRG:

#SEQ_ID         CHIP_ID       FREEMIX  CHIPMIX

sample_841 sample_843 0.00912 0.99553

sample_845 sample_856 0.01125 0.99451

sample_930 sample_833 0.00975 0.99459

sample_931 sample_834 0.01073 0.99449

sample_935 sample_838 0.00865 0.99606

sample_936 sample_839 0.00660 0.99708

sample_937 sample_840 0.00567 0.99744

sample_939 sample_842 0.00555 0.99747

sample_940 sample_844 0.01142 0.99432

sample_941 sample_845 0.00844 0.99617

sample_943 sample_847 0.00832 0.99613

bestRG:

#SEQ_ID         CHIP_ID       FREEMIX  CHIPMIX

sample_841 sample_843 0.00912 0.00846

sample_845 sample_856 0.01125 0.01097

sample_930 sample_833 0.00975 0.00890

sample_931 sample_834 0.01073 0.00994

sample_935 sample_838 0.00865 0.00816

sample_936 sample_839 0.00660 0.00609

sample_937 sample_840 0.00567 0.00559

sample_939 sample_842 0.00555 0.00613

sample_940 sample_844 0.01142 0.01117

sample_941 sample_845 0.00844 0.00793

sample_943 sample_847 0.00832 0.00798

bestSM:

#SEQ_ID         CHIP_ID       FREEMIX  CHIPMIX

sample_841 sample_843 0.00912 0.00846

sample_845 sample_856 0.01125 0.01097

sample_930 sample_833 0.00975 0.00890

sample_931 sample_834 0.01073 0.00994

sample_935 sample_838 0.00865 0.00816

sample_936 sample_839 0.00660 0.00609

sample_937 sample_840 0.00567 0.00559

sample_939 sample_842 0.00555 0.00613

sample_940 sample_844 0.01142 0.01117

sample_941 sample_845 0.00844 0.00793

sample_943 sample_847 0.00832 0.00798

Verbose output:

sample_841.log: Best Matching Individual is sample_843 with IBD = 0.991544

sample_841.log: Self Individual is sample_841 with IBD = 0.995526

sample_845.log: Best Matching Individual is sample_856 with IBD = 0.989027

sample_845.log: Self Individual is sample_845 with IBD = 0.994510

sample_930.log: Best Matching Individual is sample_833 with IBD = 0.991100

sample_930.log: Self Individual is sample_930 with IBD = 0.994592

sample_931.log: Best Matching Individual is sample_834 with IBD = 0.990062

sample_931.log: Self Individual is sample_931 with IBD = 0.994487

sample_935.log: Best Matching Individual is sample_838 with IBD = 0.991842

sample_935.log: Self Individual is sample_935 with IBD = 0.996062

sample_936.log: Best Matching Individual is sample_839 with IBD = 0.993906

sample_936.log: Self Individual is sample_936 with IBD = 0.997082

sample_937.log: Best Matching Individual is sample_840 with IBD = 0.994406

sample_937.log: Self Individual is sample_937 with IBD = 0.997440

sample_939.log: Best Matching Individual is sample_842 with IBD = 0.993873

sample_939.log: Self Individual is sample_939 with IBD = 0.997469

sample_940.log: Best Matching Individual is sample_844 with IBD = 0.988828

sample_940.log: Self Individual is sample_940 with IBD = 0.994324

sample_941.log: Best Matching Individual is sample_845 with IBD = 0.992072

sample_941.log: Self Individual is sample_941 with IBD = 0.996170

sample_943.log: Best Matching Individual is sample_847 with IBD = 0.992024

sample_943.log: Self Individual is sample_943 with IBD = 0.996127

PS: Processing of VCF: This is RNA-Seq data, so I used SNPs that overlap any annotated exon, as other SNPs will be least informative, to reduce the run time and to get accurate estimates.

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