iqbal-lab/Mykrobe-predictor

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Phelimb commented

/dev/git/Mykrobe-predictor/bin/Mykrobe.predictor.staph --file 2d.fq.9hours.fastq --install_dir ~/dev/git/Mykrobe-predictor
...
"called_variants" :{
"gyrA_S84L" :{
"R_per_cov": "93",
"S_per_cov": "0",
"R_median_cov": "2",
"S_median_cov": "0",
"conf": "12",
"induced_resistance": "Ciprofloxacin"
}

and this is what we get when we subsample to 8 hours

    "called_variants" :{
            "grlA_S80F" :{
                    "R_per_cov": "100",
                    "S_per_cov": "0",
                    "R_median_cov": "2",
                    "S_median_cov": "0",
                    "conf": "12",
            "induced_resistance": "Ciprofloxacin"
            }
iqbal-lab commented

Our mental model of the implementation says that if you detect an allele at
covg x, you should always detect it for covg >x. You may or may not call
the sample as minor/major resistant, but you should see and report the
allele. So there is a disjunct between our mental model and empirical
behaviour,

On 21 April 2015 at 10:24, Phelim Bradley notifications@github.com wrote:

/dev/git/Mykrobe-predictor/bin/Mykrobe.predictor.staph --file
2d.fq.9hours.fastq --install_dir ~/dev/git/Mykrobe-predictor
...
"called_variants" :{
"gyrA_S84L" :{
"R_per_cov": "93",
"S_per_cov": "0",
"R_median_cov": "2",
"S_median_cov": "0",
"conf": "12",
"induced_resistance": "Ciprofloxacin"
}

and this is what we get when we subsample to 8 hours

"called_variants" :{
        "grlA_S80F" :{
                "R_per_cov": "100",
                "S_per_cov": "0",
                "R_median_cov": "2",
                "S_median_cov": "0",
                "conf": "12",
        "induced_resistance": "Ciprofloxacin"
        }

—
Reply to this email directly or view it on GitHub
#63.

iqbal-lab commented

Like all the best bugs!

On 21 April 2015 at 10:43, Zamin Iqbal zam.iqbal.lab@gmail.com wrote:

Our mental model of the implementation says that if you detect an allele
at covg x, you should always detect it for covg >x. You may or may not call
the sample as minor/major resistant, but you should see and report the
allele. So there is a disjunct between our mental model and empirical
behaviour,

On 21 April 2015 at 10:24, Phelim Bradley notifications@github.com
wrote:

/dev/git/Mykrobe-predictor/bin/Mykrobe.predictor.staph --file
2d.fq.9hours.fastq --install_dir ~/dev/git/Mykrobe-predictor
...
"called_variants" :{
"gyrA_S84L" :{
"R_per_cov": "93",
"S_per_cov": "0",
"R_median_cov": "2",
"S_median_cov": "0",
"conf": "12",
"induced_resistance": "Ciprofloxacin"
}

and this is what we get when we subsample to 8 hours

"called_variants" :{
        "grlA_S80F" :{
                "R_per_cov": "100",
                "S_per_cov": "0",
                "R_median_cov": "2",
                "S_median_cov": "0",
                "conf": "12",
        "induced_resistance": "Ciprofloxacin"
        }

—
Reply to this email directly or view it on GitHub
#63.