estimation per sample in the genotype file against a single BAM file

[haroo...@gmail.com]

I ran the VerifyBamID (https://github.com/Griffan/VerifyBamID) using a multi-sample genotype in vcf format and a single DNASeq alignment file in BAM format.

First i generated the SVD Auxiliary files using a genotype file (n=6000 samples). The tool output looks like this:

NOTICE - Specified --RefVCF reference panel VCF file, doing SVD on the fly...
NOTICE - This procedure will generate SVD matrices as [RefVCF path].UD and [RefVCF path].mu
NOTICE - You may specify --SVDPrefix [RefVCF path](or --UDPath [RefVCF path].UD and --MeanPath [RefVCF path].mu) in future use
NOTICE - Number of Markers:742515

NOTICE - Number of Individuals:6000

NOTICE - Success!

Then, I used the verifybamid for regular estimation. The tool generated two files ( *.out and *.selfSM):

*.out output:

Estimation from OptimizeHeter:
Contaminating Sample PC1:-0.592266      PC2:1.27583    
Intended Sample PC1:0.0130975   PC2:-0.0114648 
Alpha:7.02389e-07

*.selfSM output:

#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
SRRXXXXX      NA      NA      742515  31596941        42.5541 7.02389e-07     -7.46403e+06    -1.17622e+07    NA      NA      NA      NA      NA      NA      NA      NA      NA      NA

My genotype file contains 6000 samples but verifybamid is displaying only 1 record in the *.selfSM file. How can I interpret the results since there is no sample ID in the genotype file is displaying in the *.selfSM.

I was wondering how can I get the estimation per sample in the genotype file against a single BAM file. 

Any advise will be appreciated.

2.6.0.0

[Hyun Min Kang]

verifyBamID2 do not match the identity with the chip data. It only performs genotype-free estimation (for now). Use the original verifyBamID to estimate contamination with external genotype data.

Hyun.

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[haroo...@gmail.com]

Thanks very much for your reply, highly appreciated.

2.6.0.0

[Rozaimi Razali]

Hi Hyun,

Use the original verifyBamID 

Do you mean the older release of verifyBamID like this one http://csg.sph.umich.edu/kang/verifyBamID/download/verifyBamID.20120620.gz? I got it from here: http://csg.sph.umich.edu/kang/verifyBamID/download/

Rozaimi

[haroo...@gmail.com]

Can we use this version?

verifyBamID 1.0.0 -- verify identity and purity of sequence data
(c) 2010 Hyun Min Kang, Goo Jun, and Goncalo Abecasis


WARNING -
Problems encountered parsing command line:

Command line parameter -h (#1) ignored


The following parameters are available.  Ones with "[]" are in effect:

Available Options
                             Input Files : --vcf [], --bam [], --subset [],
                                           --smID []
                    VCF analysis options : --genoError [1.0e-03],
                                           --minAF [0.01],
                                           --minCallRate [0.50]
   Individuals to compare with chip data : --site, --self, --best
          Chip-free optimization options : --free-none, --free-mix [ON],
                                           --free-refBias, --free-full
          With-chip optimization options : --chip-none, --chip-mix [ON],
                                           --chip-refBias, --chip-full
                    BAM analysis options : --ignoreRG, --ignoreOverlapPair,
                                           --noEOF, --precise, --minMapQ [10],
                                           --maxDepth [20], --minQ [13],
                                           --maxQ [40], --grid [0.05]
                 Modeling Reference Bias : --refRef [1.00], --refHet [0.50],
                                           --refAlt [0.00]
                          Output options : --out [], --verbos

Regards,

Haroon

2.6.0.0