[DOCKTESTERS] Sanger extended validation for 1 sample. Only differences in SNV

[Miguel Vazquez]

Thanks for your input Keiran. Indeed none of the extra or missing mutations
are marked 'PASS'.

Best

Miguel

On Fri, Dec 16, 2016 at 12:33 PM, Keiran Raine <kr2 at sanger.ac.uk> wrote:

> Hi Miguel,
>
> Please be aware that we agreed to include the last version of the
> algorithms used in the core analysis for the final docker (as there were
> fixes along the way).
>
> There were several versions of the core SNV caller fixing edge cases.  I
> don't see these discrepancies being an issue, especially if they aren't
> marked as 'PASS'.
>
> It's theoretically possible for some of these to be floating-point
> differences (esp. if different CPU arch), this can cause a call to flip
> between the SNP and SUB output if very close to the cut-off.
>
> Sending the physical VCF records (with the VCF header) for these from the
> relevant run (missing from the old run, Extra from the new) would allow a
> confirmation, but as I say if they aren't marked 'PASS' we wouldn't be
> planning to do any thing about them.
>
> Regards,
>
> Keiran Raine
> Principal Bioinformatician
> Cancer Genome Project
> Wellcome Trust Sanger Institute
>
> kr2 at sanger.ac.uk
> Tel:+44 (0)1223 834244 Ext: 4983 <+44%201223%20834244>
> Office: H104
>
> On 16 Dec 2016, at 10:50, Miguel Vazquez <miguel.vazquez at cnio.es> wrote:
>
> Dear Christina and Keiran,
>
> I've extended the analysis also for the Sanger workflow. I only have one
> sample (DO50311) since the second one (DO52140) its still computing since
> December 8 (8 days)
>
> Keiran I believed you asked me about how indels and CNVs matched. Is this
> what you needed?
>
> All matches except for the +1 -14 differences I reported before
>
> Best regards
>
> Miguel
>
> Report
> ~~~~~
>
> Comparison of somatic.cnv for DO50311 using Sanger
> ---
> Common: 138
> Extra: 0
> Missing: 0
>
>
> Comparison of somatic.indel for DO50311 using Sanger
> ---
> Common: 812487
> Extra: 0
> Missing: 0
>
>
> Comparison of somatic.snv.mnv for DO50311 using Sanger
> ---
> Common: 156299
> Extra: 1
>     - Example: Y:58885197:A:G
> Missing: 14
>     - Example: 1:102887902:A:T,1:143165228:C:G,16:87047601:A:C
>
>
> Comparison of somatic.sv for DO50311 using Sanger
> ---
> Common: 260
> Extra: 0
> Missing: 0
>
>
> *Note. To make matching more stringent in indels I've added the reference
> to the mutation code end up comparing. This extends to SNV as well so where
> previously I wrote *16:87047601:C I* now write *16:87047601:A:C.* The
> extremely thorough reader will notice that the reports for DKFZ bellow show
> the discrepancies in CNV not following this new format. I've introduced
> this afterwards, but the results have not changed for DKFZ; I've checked.
>
> On Fri, Dec 16, 2016 at 11:07 AM, Miguel Vazquez <miguel.vazquez at cnio.es>
> wrote:
>
>> Excuse me, obviously I meant
>>
>> *For the two samples all matches perfectly except CNV where we find some
>> large differences. *
>>
>> On Fri, Dec 16, 2016 at 11:05 AM, Miguel Vazquez <miguel.vazquez at cnio.es>
>> wrote:
>>
>>> Hi Christina et al.
>>>
>>> Like you asked me I've extended the validation from SNV to Indel and SNV
>>> and also for germline
>>>
>>> For the two samples all matches perfectly except SNV where we find some
>>> large differences.
>>>
>>> Best regards
>>>
>>> Miguel
>>>
>>> Report
>>> ~~~~~
>>>
>>> Comparison of germline.indel for DO50311 using DKFZ
>>> ---
>>> Common: 709060
>>> Extra: 0
>>> Missing: 0
>>>
>>>
>>> Comparison of germline.snv.mnv for DO50311 using DKFZ
>>> ---
>>> Common: 3850992
>>> Extra: 0
>>> Missing: 0
>>>
>>>
>>> Comparison of somatic.cnv for DO50311 using DKFZ
>>> ---
>>> Common: 731
>>> Extra: 213
>>>     - Example: 10:132510034:<DEL>,10:20596801
>>> :<NEUTRAL>,10:47674883:<NEUTRAL>
>>> Missing: 190
>>>     - Example: 10:100891940:<NEUTRAL>,10:1049
>>> 75905:<NEUTRAL>,10:119704960:<NEUTRAL>
>>>
>>>
>>> Comparison of somatic.indel for DO50311 using DKFZ
>>> ---
>>> Common: 26469
>>> Extra: 0
>>> Missing: 0
>>>
>>>
>>> Comparison of somatic.snv.mnv for DO50311 using DKFZ
>>> ---
>>> Common: 51087
>>> Extra: 0
>>> Missing: 0
>>>
>>>
>>> Comparison of germline.indel for DO52140 using DKFZ
>>> ---
>>> Common: 706572
>>> Extra: 0
>>> Missing: 0
>>>
>>>
>>> Comparison of germline.snv.mnv for DO52140 using DKFZ
>>> ---
>>> Common: 3833896
>>> Extra: 0
>>> Missing: 0
>>>
>>>
>>> Comparison of somatic.cnv for DO52140 using DKFZ
>>> ---
>>> Common: 275
>>> Extra: 94
>>>     - Example: 1:106505931:<LOH>,1:109068899:<DEL>,1:109359995:<DEL>
>>> Missing: 286
>>>     - Example: 10:88653561:<LOH>,11:179192:<LOH>,11:38252006:<LOH>
>>>
>>>
>>> Comparison of somatic.indel for DO52140 using DKFZ
>>> ---
>>> Common: 19347
>>> Extra: 0
>>> Missing: 0
>>>
>>>
>>> Comparison of somatic.snv.mnv for DO52140 using DKFZ
>>> ---
>>> Common: 37160
>>> Extra: 0
>>> Missing: 0
>>>
>>>
>>
>
>
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