Report all samples from the genotype file

[Timothee Cezard]

Hi 

When comparing a bam file against multiple sample vcf file, I see from the log that it compare the reads against each individuals genotype.

However the output only contains the best matching individuals.

I am wondering if there is an option to report the results of each individuals present in the vcf file.

Is it something you would consider implementing ?

Cheers

Tim

[Hyun Min Kang]

The log file have all the information for each individual, but the output may not pretty. Would it be something you could try to see first?

Thanks,

Hyun.

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[CEZARD Timothe]

Thank you Hyun for your quick reply.

I saw the output in the log but was not completely sure how to convert the Optimal fIDB to CHIPMIX. 

Is it just :

CHIPMIX = 1 – fIDB

Cheers

Tim

[Hyun Min Kang]

That is correct.

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

[Nathalie Lai]

hello,

Why don't I find the same fIBD when comparing Sample 1 to Sample2, and Sample 2 to Sample 1?

VerifyBamID on Sample_2 against VCF containing genotype of 6 individuals:

Comparing with individual Sample_1.. Optimal fIBD = 0.985558, LLK0 = 314.857806, LLK1 = 311.413558 for readgroup -1

VerifyBamID on Sample_1 against VCF containing genotype of same 6 individuals:

Comparing with individual Sample_2.. Optimal fIBD = 0.999897, LLK0 = 293.393406, LLK1 = 293.401090 for readgroup -1

Also why isnt the fIBD of a sample's BAM against himself = 100% if the genotype in the VCF was calculated on that same BAM file?

Thanks!