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

[Miguel Vazquez]

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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