Replicate Samples
2016_08_23 Data Snapshot
In many instances there is more than one aliquot for a given combination of individual, platform, and data type. However, only one aliquot may be ingested into Firehose. Therefore, a set of precedence rules are applied to select the most scientifically advantageous one among them. Two filters are applied to achieve this aim: an Analyte Replicate Filter and a Sort Replicate Filter.
Analyte Replicate Filter
The following precedence rules are applied when the aliquots have differing analytes. For RNA aliquots, T analytes are dropped in preference to H and R analytes, since T is the inferior extraction protocol. If H and R are encountered, H is the chosen analyte. This is somewhat arbitrary and subject to change, since it is not clear at present whether H or R is the better protocol. If there are multiple aliquots associated with the chosen RNA analyte, the aliquot with the later plate number is chosen. For DNA aliquots, D analytes (native DNA) are preferred over G, W, or X (whole-genome amplified) analytes, unless the G, W, or X analyte sample has a higher plate number.
Sort Replicate Filter
The following precedence rules are applied when the analyte filter still produces more than one sample. The sort filter chooses the aliquot with the highest lexicographical sort value, to ensure that the barcode with the highest portion and/or plate number is selected when all other barcode fields are identical.
Table 1. Get Full Table
| Participant.Id | Tumor.Type | Annotation | Filter.Reason | Removed.Samples | Chosen.Sample |
|---|---|---|---|---|---|
| TCGA-06-0122 | GBM | CNV__snp6 | Analyte Replicate Filter | TCGA-06-0122-10A-01D-0214-01 | TCGA-06-0122-10A-01G-0289-01 |
| TCGA-06-0122 | GBM | CNV_no_germline__snp6 | Analyte Replicate Filter | TCGA-06-0122-10A-01D-0214-01 | TCGA-06-0122-10A-01G-0289-01 |
| TCGA-06-0122 | GBM | CNV__snp6 | Analyte Replicate Filter | TCGA-06-0122-01A-01D-0214-01 | TCGA-06-0122-01A-01G-0289-01 |
| TCGA-06-0122 | GBM | CNV_no_germline__snp6 | Analyte Replicate Filter | TCGA-06-0122-01A-01D-0214-01 | TCGA-06-0122-01A-01G-0289-01 |
| TCGA-06-0124 | GBM | CNV__snp6 | Analyte Replicate Filter | TCGA-06-0124-10A-01D-0214-01 | TCGA-06-0124-10A-01G-0289-01 |
| TCGA-06-0124 | GBM | CNV_no_germline__snp6 | Analyte Replicate Filter | TCGA-06-0124-10A-01D-0214-01 | TCGA-06-0124-10A-01G-0289-01 |
| TCGA-06-0124 | GBM | CNV__snp6 | Analyte Replicate Filter | TCGA-06-0124-01A-01D-0214-01 | TCGA-06-0124-01A-01G-0289-01 |
| TCGA-06-0124 | GBM | CNV_no_germline__snp6 | Analyte Replicate Filter | TCGA-06-0124-01A-01D-0214-01 | TCGA-06-0124-01A-01G-0289-01 |
| TCGA-06-0125 | GBM | CNV__snp6 | Analyte Replicate Filter | TCGA-06-0125-10A-01D-0214-01 | TCGA-06-0125-10A-01G-0289-01 |
| TCGA-06-0125 | GBM | CNV_no_germline__snp6 | Analyte Replicate Filter | TCGA-06-0125-10A-01D-0214-01 | TCGA-06-0125-10A-01G-0289-01 |
| TCGA-06-0125 | GBM | CNV__snp6 | Analyte Replicate Filter | TCGA-06-0125-01A-01D-0214-01 | TCGA-06-0125-01A-01G-0289-01 |
| TCGA-06-0125 | GBM | CNV_no_germline__snp6 | Analyte Replicate Filter | TCGA-06-0125-01A-01D-0214-01 | TCGA-06-0125-01A-01G-0289-01 |
| TCGA-06-0126 | GBM | CNV__snp6 | Analyte Replicate Filter | TCGA-06-0126-10A-01D-0214-01 | TCGA-06-0126-10A-01G-0289-01 |
| TCGA-06-0126 | GBM | CNV_no_germline__snp6 | Analyte Replicate Filter | TCGA-06-0126-10A-01D-0214-01 | TCGA-06-0126-10A-01G-0289-01 |
| TCGA-06-0126 | GBM | CNV__snp6 | Analyte Replicate Filter | TCGA-06-0126-01A-01D-0214-01 | TCGA-06-0126-01A-01G-0289-01 |
| TCGA-06-0126 | GBM | CNV_no_germline__snp6 | Analyte Replicate Filter | TCGA-06-0126-01A-01D-0214-01 | TCGA-06-0126-01A-01G-0289-01 |
| TCGA-06-0128 | GBM | CNV__snp6 | Analyte Replicate Filter | TCGA-06-0128-10A-01D-0214-01 | TCGA-06-0128-10A-01G-0289-01 |
| TCGA-06-0128 | GBM | CNV_no_germline__snp6 | Analyte Replicate Filter | TCGA-06-0128-10A-01D-0214-01 | TCGA-06-0128-10A-01G-0289-01 |
| TCGA-06-0128 | GBM | CNV__snp6 | Analyte Replicate Filter | TCGA-06-0128-01A-01D-0214-01 | TCGA-06-0128-01A-01G-0289-01 |
| TCGA-06-0128 | GBM | CNV_no_germline__snp6 | Analyte Replicate Filter | TCGA-06-0128-01A-01D-0214-01 | TCGA-06-0128-01A-01G-0289-01 |
| TCGA-06-0129 | GBM | CNV__snp6 | Analyte Replicate Filter | TCGA-06-0129-10A-01D-0214-01 | TCGA-06-0129-10A-01G-0289-01 |
| TCGA-06-0129 | GBM | CNV_no_germline__snp6 | Analyte Replicate Filter | TCGA-06-0129-10A-01D-0214-01 | TCGA-06-0129-10A-01G-0289-01 |
| TCGA-06-0129 | GBM | CNV__snp6 | Analyte Replicate Filter | TCGA-06-0129-01A-01D-0214-01 | TCGA-06-0129-01A-01G-0289-01 |
| TCGA-06-0129 | GBM | CNV_no_germline__snp6 | Analyte Replicate Filter | TCGA-06-0129-01A-01D-0214-01 | TCGA-06-0129-01A-01G-0289-01 |
| TCGA-06-0130 | GBM | CNV__snp6 | Analyte Replicate Filter | TCGA-06-0130-10A-01D-0214-01 | TCGA-06-0130-10A-01G-0289-01 |
| TCGA-06-0130 | GBM | CNV_no_germline__snp6 | Analyte Replicate Filter | TCGA-06-0130-10A-01D-0214-01 | TCGA-06-0130-10A-01G-0289-01 |
| TCGA-06-0130 | GBM | CNV__snp6 | Analyte Replicate Filter | TCGA-06-0130-01A-01D-0214-01 | TCGA-06-0130-01A-01G-0289-01 |
| TCGA-06-0130 | GBM | CNV_no_germline__snp6 | Analyte Replicate Filter | TCGA-06-0130-01A-01D-0214-01 | TCGA-06-0130-01A-01G-0289-01 |
| TCGA-06-0138 | GBM | CNV__snp6 | Analyte Replicate Filter | TCGA-06-0138-01A-01D-0236-01 | TCGA-06-0138-01A-02D-0236-01 |
| TCGA-06-0138 | GBM | CNV_no_germline__snp6 | Analyte Replicate Filter | TCGA-06-0138-01A-01D-0236-01 | TCGA-06-0138-01A-02D-0236-01 |
| TCGA-06-0139 | GBM | CNV__snp6 | Analyte Replicate Filter | TCGA-06-0139-01A-01D-0214-01 | TCGA-06-0139-01B-05D-0214-01 |
| TCGA-06-0139 | GBM | CNV_no_germline__snp6 | Analyte Replicate Filter | TCGA-06-0139-01A-01D-0214-01 | TCGA-06-0139-01B-05D-0214-01 |
| TCGA-06-0141 | GBM | CNV__snp6 | Analyte Replicate Filter | TCGA-06-0141-10A-01D-0214-01 | TCGA-06-0141-10A-01G-0289-01 |
| TCGA-06-0141 | GBM | CNV_no_germline__snp6 | Analyte Replicate Filter | TCGA-06-0141-10A-01D-0214-01 | TCGA-06-0141-10A-01G-0289-01 |
| TCGA-06-0141 | GBM | CNV__snp6 | Analyte Replicate Filter | TCGA-06-0141-01A-01D-0214-01 | TCGA-06-0141-01A-01G-0289-01 |
| TCGA-06-0141 | GBM | CNV_no_germline__snp6 | Analyte Replicate Filter | TCGA-06-0141-01A-01D-0214-01 | TCGA-06-0141-01A-01G-0289-01 |
| TCGA-06-0143 | GBM | CNV__snp6 | Analyte Replicate Filter | TCGA-06-0143-10A-01D-0214-01 | TCGA-06-0143-10A-01G-0289-01 |
| TCGA-06-0143 | GBM | CNV_no_germline__snp6 | Analyte Replicate Filter | TCGA-06-0143-10A-01D-0214-01 | TCGA-06-0143-10A-01G-0289-01 |
| TCGA-06-0143 | GBM | CNV__snp6 | Analyte Replicate Filter | TCGA-06-0143-01A-01D-0214-01 | TCGA-06-0143-01A-01G-0289-01 |
| TCGA-06-0143 | GBM | CNV_no_germline__snp6 | Analyte Replicate Filter | TCGA-06-0143-01A-01D-0214-01 | TCGA-06-0143-01A-01G-0289-01 |
| TCGA-06-0147 | GBM | CNV__snp6 | Analyte Replicate Filter | TCGA-06-0147-10A-01D-0214-01 | TCGA-06-0147-10A-01D-0237-01 |
| TCGA-06-0147 | GBM | CNV_no_germline__snp6 | Analyte Replicate Filter | TCGA-06-0147-10A-01D-0214-01 | TCGA-06-0147-10A-01D-0237-01 |
| TCGA-06-0147 | GBM | CNV__snp6 | Analyte Replicate Filter | TCGA-06-0147-01A-01D-0214-01 | TCGA-06-0147-01A-02D-0236-01 |
| TCGA-06-0147 | GBM | CNV_no_germline__snp6 | Analyte Replicate Filter | TCGA-06-0147-01A-01D-0214-01 | TCGA-06-0147-01A-02D-0236-01 |
| TCGA-06-0154 | GBM | CNV__snp6 | Analyte Replicate Filter | TCGA-06-0154-01A-02D-0236-01 | TCGA-06-0154-01A-03D-0236-01 |
| TCGA-06-0154 | GBM | CNV_no_germline__snp6 | Analyte Replicate Filter | TCGA-06-0154-01A-02D-0236-01 | TCGA-06-0154-01A-03D-0236-01 |
| TCGA-06-0156 | GBM | mRNA__counts__FPKM | Analyte Replicate Filter | TCGA-06-0156-01A-02R-1849-01 | TCGA-06-0156-01A-03R-1849-01 |
| TCGA-06-0156 | GBM | mRNA__geneExpNormed__FPKM | Analyte Replicate Filter | TCGA-06-0156-01A-02R-1849-01 | TCGA-06-0156-01A-03R-1849-01 |
| TCGA-06-0156 | GBM | mRNA__geneExp__FPKM | Analyte Replicate Filter | TCGA-06-0156-01A-02R-1849-01 | TCGA-06-0156-01A-03R-1849-01 |
| TCGA-06-0166 | GBM | CNV__snp6 | Analyte Replicate Filter | TCGA-06-0166-01A-01D-0236-01 | TCGA-06-0166-01A-01G-0289-01 |
| TCGA-06-0166 | GBM | CNV_no_germline__snp6 | Analyte Replicate Filter | TCGA-06-0166-01A-01D-0236-01 | TCGA-06-0166-01A-01G-0289-01 |
| TCGA-06-0168 | GBM | CNV__snp6 | Analyte Replicate Filter | TCGA-06-0168-01A-01D-0236-01 | TCGA-06-0168-01A-02D-0236-01 |
| TCGA-06-0168 | GBM | CNV_no_germline__snp6 | Analyte Replicate Filter | TCGA-06-0168-01A-01D-0236-01 | TCGA-06-0168-01A-02D-0236-01 |
| TCGA-06-0176 | GBM | CNV__snp6 | Analyte Replicate Filter | TCGA-06-0176-01A-02D-0236-01 | TCGA-06-0176-01A-03D-0236-01 |
| TCGA-06-0176 | GBM | CNV_no_germline__snp6 | Analyte Replicate Filter | TCGA-06-0176-01A-02D-0236-01 | TCGA-06-0176-01A-03D-0236-01 |
| TCGA-06-0210 | GBM | CNV__snp6 | Analyte Replicate Filter | TCGA-06-0210-01A-01D-0236-01 | TCGA-06-0210-01B-01D-0236-01 |
| TCGA-06-0210 | GBM | CNV_no_germline__snp6 | Analyte Replicate Filter | TCGA-06-0210-01A-01D-0236-01 | TCGA-06-0210-01B-01D-0236-01 |
| TCGA-06-0211 | GBM | CNV__snp6 | Analyte Replicate Filter | TCGA-06-0211-01A-01D-0236-01 | TCGA-06-0211-01B-01D-0236-01 |
| TCGA-06-0211 | GBM | CNV_no_germline__snp6 | Analyte Replicate Filter | TCGA-06-0211-01A-01D-0236-01 | TCGA-06-0211-01B-01D-0236-01 |
| TCGA-06-0211 | GBM | mRNA__counts__FPKM | Analyte Replicate Filter | TCGA-06-0211-01A-01R-1849-01 | TCGA-06-0211-01B-01R-1849-01 |
| TCGA-06-0211 | GBM | mRNA__geneExpNormed__FPKM | Analyte Replicate Filter | TCGA-06-0211-01A-01R-1849-01 | TCGA-06-0211-01B-01R-1849-01 |
| TCGA-06-0211 | GBM | mRNA__geneExp__FPKM | Analyte Replicate Filter | TCGA-06-0211-01A-01R-1849-01 | TCGA-06-0211-01B-01R-1849-01 |
| TCGA-06-0216 | GBM | CNV__snp6 | Analyte Replicate Filter | TCGA-06-0216-10A-01D-0237-01 | TCGA-06-0216-10A-01D-0333-01 |
| TCGA-06-0216 | GBM | CNV_no_germline__snp6 | Analyte Replicate Filter | TCGA-06-0216-10A-01D-0237-01 | TCGA-06-0216-10A-01D-0333-01 |
| TCGA-06-0216 | GBM | CNV__snp6 | Analyte Replicate Filter | TCGA-06-0216-01A-01D-0236-01 | TCGA-06-0216-01B-01D-0333-01 |
| TCGA-06-0216 | GBM | CNV_no_germline__snp6 | Analyte Replicate Filter | TCGA-06-0216-01A-01D-0236-01 | TCGA-06-0216-01B-01D-0333-01 |