A guideline to interpret output files

[Daekwan Seo]

• At first, I would like to many thanks for the nice tool for contamination checking in sequencing data.
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• As mentioned in interpret output files,
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• "When genotype data is not available but allele-frequency-based estimates of [FREEMIX] >= 0.03 and [FREELK1]-[FREELK0] is large, then it is possible that the sample is contaminated with other sample. We recommend to use per-sample data rather than per-lane data for checking this for low coverage data, because the inference will be more confident when there are large number of bases with depth 2 or higher."

Can you let us know a kind of threshold for FREELK1-FREELK0? I mean, how large value can lead me to decide my sample is contaminated sample?

Best,

Daekwan

[Hyun Min Kang]

I would use something like 12, which correspond to pvalue of 1e-6 when chisq is used as null distribution. This might be still too lenient, and something heuristic, like 100 might be better in terms of specificity

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[Daekwan Seo]

Thanks

[raqs...@gmail.com]

Hi,

I have been getting negative values (all kinds of range) for FREELK1 - FREELK0 independently of the FREEMIX value.

Command line used is 

verifyBamID --vcf $1 --bam $2 --out $3 --verbose --ignoreRG --site --minQ 20

Two example outputs from different BAMs and VCFs:

 #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

SI_2 ALL NA 11341430 9579343 0.84 0.49992 3276580.38 3362001.50 NA NA NA NA NA NA NA NA NA NA

or

#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

79_C4_CD4naive ALL NA 2615527 438963 0.17 0.00468 171452.74 171803.39 NA NA NA NA NA NA NA NA NA NA

Best regards,

Raquel