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@deflaux
deflaux committed Jun 9, 2017
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98 changes: 51 additions & 47 deletions R/PlatinumGenomes-QC/Data-Overview.md
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Expand Up @@ -49,7 +49,10 @@ result <- DisplayAndDispatchQuery("./sql/variant-level-data-for-brca1.sql",
```

```
# Retrieve variant-level information for BRCA1 variants.
#standardSQL
--
-- Retrieve variant-level information for BRCA1 variants.
--
SELECT
reference_name,
start,
Expand All @@ -71,20 +74,18 @@ ORDER BY
start,
alt_concat
```
Number of rows returned by this query: **335**.
Number of rows returned by this query: **281**.

Displaying the first few rows of the dataframe of results:
<!-- html table generated in R 3.2.3 by xtable 1.8-2 package -->
<!-- Wed Nov 23 11:34:46 2016 -->
<table border=1>
<tr> <th> reference_name </th> <th> start </th> <th> end </th> <th> ref </th> <th> alt_concat </th> <th> quality </th> <th> filters </th> <th> names </th> <th> num_samples </th> </tr>
<tr> <td> chr17 </td> <td align="right"> 41196407 </td> <td align="right"> 41196408 </td> <td> G </td> <td> A </td> <td align="right"> 733.47 </td> <td> PASS </td> <td> </td> <td align="right"> 7 </td> </tr>
<tr> <td> chr17 </td> <td align="right"> 41196820 </td> <td align="right"> 41196822 </td> <td> CT </td> <td> C </td> <td align="right"> 63.74 </td> <td> LowQD </td> <td> </td> <td align="right"> 1 </td> </tr>
<tr> <td> chr17 </td> <td align="right"> 41196820 </td> <td align="right"> 41196823 </td> <td> CTT </td> <td> C,CT </td> <td align="right"> 314.59 </td> <td> PASS </td> <td> </td> <td align="right"> 3 </td> </tr>
<tr> <td> chr17 </td> <td align="right"> 41196840 </td> <td align="right"> 41196841 </td> <td> G </td> <td> T </td> <td align="right"> 85.68 </td> <td> TruthSensitivityTranche99.90to100.00,LowQD </td> <td> </td> <td align="right"> 2 </td> </tr>
<tr> <td> chr17 </td> <td align="right"> 41197273 </td> <td align="right"> 41197274 </td> <td> C </td> <td> A </td> <td align="right"> 1011.08 </td> <td> PASS </td> <td> </td> <td align="right"> 7 </td> </tr>
<tr> <td> chr17 </td> <td align="right"> 41197938 </td> <td align="right"> 41197939 </td> <td> A </td> <td> AT </td> <td align="right"> 86.95 </td> <td> LowQD </td> <td> </td> <td align="right"> 3 </td> </tr>
</table>

|reference_name | start| end|ref |alt_concat | quality|filters |names | num_samples|
|:--------------|--------:|--------:|:---|:----------|-------:|:-------------------------------------------------|:-----|-----------:|
|chr17 | 41196407| 41196408|G |A | 733.47|PASS | | 3|
|chr17 | 41196820| 41196823|CTT |C,CT | 287.18|PASS | | 1|
|chr17 | 41197273| 41197274|C |A | 1011.08|PASS | | 3|
|chr17 | 41197957| 41197958|G |T | 178.48|TruthSensitivityTranche99.90to100.00 | | 4|
|chr17 | 41198182| 41198183|A |C | 98.02|TruthSensitivityTranche99.00to99.90 | | 1|
|chr17 | 41198186| 41198187|A |C | 7.68|TruthSensitivityTranche99.90to100.00,LowGQX,LowQD | | 4|

These are the variant-level fields common to all variant sets exported to BigQuery from Google Genomics. There are often dataset-specific variant-level fields as well. For more information about additional fields, see the schema for the table being queried.

Expand All @@ -101,7 +102,10 @@ result <- DisplayAndDispatchQuery("./sql/non-variant-segments-brca1.sql",
```

```
# Retrieve non-variant segments for BRCA1.
#standardSQL
--
-- Retrieve non-variant segments for BRCA1.
--
SELECT
call.call_set_name,
(SELECT STRING_AGG(CAST(gt AS STRING)) from UNNEST(call.genotype) gt) AS genotype,
Expand All @@ -123,20 +127,18 @@ ORDER BY
LIMIT
10000
```
Number of rows returned by this query: **10000**.
Number of rows returned by this query: **8123**.

Displaying the first few rows of the dataframe of results:
<!-- html table generated in R 3.2.3 by xtable 1.8-2 package -->
<!-- Wed Nov 23 11:34:53 2016 -->
<table border=1>
<tr> <th> call_set_name </th> <th> genotype </th> <th> reference_name </th> <th> start </th> <th> end </th> <th> ref </th> <th> alt_concat </th> </tr>
<tr> <td> not displayed </td> <td> 0,0 </td> <td> chr17 </td> <td align="right"> 41196313 </td> <td align="right"> 41196746 </td> <td> G </td> <td> </td> </tr>
<tr> <td> not displayed </td> <td> 0,0 </td> <td> chr17 </td> <td align="right"> 41196321 </td> <td align="right"> 41196381 </td> <td> T </td> <td> </td> </tr>
<tr> <td> not displayed </td> <td> 0,0 </td> <td> chr17 </td> <td align="right"> 41196322 </td> <td align="right"> 41196356 </td> <td> G </td> <td> </td> </tr>
<tr> <td> not displayed </td> <td> 0,0 </td> <td> chr17 </td> <td align="right"> 41196337 </td> <td align="right"> 41196620 </td> <td> T </td> <td> </td> </tr>
<tr> <td> not displayed </td> <td> 0,0 </td> <td> chr17 </td> <td align="right"> 41196339 </td> <td align="right"> 41196489 </td> <td> C </td> <td> </td> </tr>
<tr> <td> not displayed </td> <td> 0,0 </td> <td> chr17 </td> <td align="right"> 41196349 </td> <td align="right"> 41196417 </td> <td> A </td> <td> </td> </tr>
</table>

|call_set_name |genotype |reference_name | start| end|ref |alt_concat |
|:-------------|:--------|:--------------|--------:|--------:|:---|:----------|
|not displayed |0,0 |chr17 | 41196321| 41196381|T | |
|not displayed |0,0 |chr17 | 41196349| 41196417|A | |
|not displayed |0,0 |chr17 | 41196369| 41196407|T | |
|not displayed |0,0 |chr17 | 41196376| 41196621|T | |
|not displayed |0,0 |chr17 | 41196381| 41196407|T | |
|not displayed |0,0 |chr17 | 41196408| 41196543|G | |

When the data contains non-variant segments, for any analyses that require us to know for example _"how many samples do and do not have a particular SNP?"_, we'll need to make sure that the non-variant segments are considered in addition to the variants.

Expand All @@ -157,7 +159,10 @@ result <- DisplayAndDispatchQuery("./sql/characterize-alts.sql",
```

```
# Check whether variants are only SNPs and INDELs, with no special characters.
#standardSQL
--
-- Check whether variants are only SNPs and INDELs, with no special characters.
--
SELECT
COUNT(1) AS number_of_variant_records,
REGEXP_CONTAINS(alt,
Expand All @@ -175,12 +180,10 @@ GROUP BY
Number of rows returned by this query: **1**.

Displaying the first few rows of the dataframe of results:
<!-- html table generated in R 3.2.3 by xtable 1.8-2 package -->
<!-- Wed Nov 23 11:34:56 2016 -->
<table border=1>
<tr> <th> number_of_variant_records </th> <th> alt_contains_no_special_characters </th> <th> max_ref_len </th> <th> max_alt_len </th> </tr>
<tr> <td align="right"> 12634588 </td> <td> TRUE </td> <td align="right"> 56 </td> <td align="right"> 47 </td> </tr>
</table>

| number_of_variant_records|alt_contains_no_special_characters | max_ref_len| max_alt_len|
|-------------------------:|:----------------------------------|-----------:|-----------:|
| 11162053|TRUE | 56| 44|

> In the case of Platinum Genomes we see from the query results that there are no special charaters in alternate_bases and the maximum length is ~50 base pairs, so just SNPs and small INDELs.
Expand All @@ -197,7 +200,10 @@ result <- DisplayAndDispatchQuery("./sql/characterize-genotypes.sql",
```

```
# Query to show the variety of genotypes.
#standardSQL
--
-- Query to show the variety of genotypes.
--
SELECT
genotype,
COUNT(genotype) AS genotype_count
Expand All @@ -215,19 +221,17 @@ ORDER BY
Number of rows returned by this query: **8**.

Displaying the first few rows of the dataframe of results:
<!-- html table generated in R 3.2.3 by xtable 1.8-2 package -->
<!-- Wed Nov 23 11:34:58 2016 -->
<table border=1>
<tr> <th> genotype </th> <th> genotype_count </th> </tr>
<tr> <td> 0,0 </td> <td align="right"> 771631170 </td> </tr>
<tr> <td> 0,1 </td> <td align="right"> 65193851 </td> </tr>
<tr> <td> 1,1 </td> <td align="right"> 30576582 </td> </tr>
<tr> <td> -1 </td> <td align="right"> 8617093 </td> </tr>
<tr> <td> 0 </td> <td align="right"> 7824166 </td> </tr>
<tr> <td> -1,-1 </td> <td align="right"> 2935215 </td> </tr>
<tr> <td> 1,2 </td> <td align="right"> 657906 </td> </tr>
<tr> <td> 1 </td> <td align="right"> 21613 </td> </tr>
</table>

|genotype | genotype_count|
|:--------|--------------:|
|0,0 | 268837097|
|0,1 | 22872404|
|1,1 | 10796056|
|-1 | 3024578|
|0 | 2750341|
|-1,-1 | 1033653|
|1,2 | 230089|
|1 | 7473|


> In the case of Platinum Genomes we see from the query results the variety of genotypes:
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