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fpbarthel / GLASS

GLASS consortium
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Missing M2 calls #105

Closed fpbarthel closed 5 years ago

fpbarthel commented 5 years ago

For a select number of aliquots we seem to be missing M2 calls. Still unsure as to why:

GLSS-MD-0025-R1-01D-WXS-SMN43I
GLSS-MD-0025-TP-01D-WXS-F3H10V
GLSS-MD-0112-TP-01D-WXS-P1B0I2
GLSS-SM-R098-R2-01D-WXS-462GI8
GLSS-SM-R101-R1-02D-WXS-PUTOC9
GLSS-SM-R101-TP-02D-WXS-TKL136
GLSS-SM-R105-R2-01D-WXS-Y9SY6I
GLSS-SM-R110-TP-02D-WXS-BQFEME
TCGA-06-0125-R1-11D-WXS-8Q4RKD
TCGA-06-0125-TP-01D-WXS-Z67AVH
TCGA-06-0152-R1-01D-WXS-MONTUP
TCGA-06-0152-TP-02D-WXS-6DXTU8
TCGA-06-0171-R1-11D-WXS-87WAQK
TCGA-06-0171-TP-02D-WXS-CY280C
TCGA-06-0190-R1-01D-WXS-ODJETQ
TCGA-06-0210-R1-01D-WXS-4MJVD2
TCGA-06-0211-R1-02D-WXS-X1GNKU
TCGA-06-0211-R1-03D-WXS-M22HJ0
TCGA-06-0211-R2-02D-WXS-KTDRP8
TCGA-06-0211-TP-01D-WXS-AS2XJL
TCGA-06-0221-R1-11D-WXS-UAUEGN
TCGA-06-0221-TP-01D-WXS-9K3HSY
TCGA-14-1034-R1-01D-WGS-L9V6H0
TCGA-14-1402-R1-01D-WXS-QGNTYA
TCGA-19-0957-TP-01D-WXS-H59SRY
TCGA-19-1389-R1-21D-WXS-YNQ3L5
TCGA-19-4065-R1-11D-WXS-ET7919
TCGA-19-4065-TP-01D-WXS-FK6Q8U
fpbarthel commented 5 years ago

Issue solved, these seem to be updated barcodes that were not updated in the called variants table.

REFRESH MATERIALIZED VIEW analysis.called_genotypes;

Should resolve this issue.

fpbarthel commented 5 years ago

Reopening, refreshing the table didn't fix this for all aliquots, and most are still wrong:

GLSS-SM-R098-R2-01D-WXS-462GI8
GLSS-SM-R101-R1-02D-WXS-PUTOC9
GLSS-SM-R101-TP-02D-WXS-TKL136
GLSS-SM-R105-R2-01D-WXS-Y9SY6I
GLSS-SM-R110-TP-02D-WXS-BQFEME
TCGA-06-0125-R1-11D-WXS-8Q4RKD
TCGA-06-0125-TP-01D-WXS-Z67AVH
TCGA-06-0152-R1-01D-WXS-MONTUP
TCGA-06-0152-TP-02D-WXS-6DXTU8
TCGA-06-0171-R1-11D-WXS-87WAQK
TCGA-06-0171-TP-02D-WXS-CY280C
TCGA-06-0190-R1-01D-WXS-ODJETQ
TCGA-06-0210-R1-01D-WXS-4MJVD2
TCGA-06-0211-R1-02D-WXS-X1GNKU
TCGA-06-0211-R1-03D-WXS-M22HJ0
TCGA-06-0211-R2-02D-WXS-KTDRP8
TCGA-06-0211-TP-01D-WXS-AS2XJL
TCGA-06-0221-R1-11D-WXS-UAUEGN
TCGA-06-0221-TP-01D-WXS-9K3HSY
TCGA-14-1402-R1-01D-WXS-QGNTYA
TCGA-19-0957-TP-01D-WXS-H59SRY
TCGA-19-1389-R1-21D-WXS-YNQ3L5
TCGA-19-4065-R1-11D-WXS-ET7919
TCGA-19-4065-TP-01D-WXS-FK6Q8U
fpbarthel commented 5 years ago

Temporarily resolving by blocking the remaining samples. To be resolved later.

UPDATE analysis.blocklist SET coverage_exclusion = 'block' AND coverage_exclusion_reason = 'm2_calls_missing' WHERE aliquot_barcode = 'GLSS-SM-R098-R2-01D-WXS-462GI8';
UPDATE analysis.blocklist SET coverage_exclusion = 'block' AND coverage_exclusion_reason = 'm2_calls_missing' WHERE aliquot_barcode = 'GLSS-SM-R101-R1-02D-WXS-PUTOC9';
UPDATE analysis.blocklist SET coverage_exclusion = 'block' AND coverage_exclusion_reason = 'm2_calls_missing' WHERE aliquot_barcode = 'GLSS-SM-R101-TP-02D-WXS-TKL136';
UPDATE analysis.blocklist SET coverage_exclusion = 'block' AND coverage_exclusion_reason = 'm2_calls_missing' WHERE aliquot_barcode = 'GLSS-SM-R105-R2-01D-WXS-Y9SY6I';
UPDATE analysis.blocklist SET coverage_exclusion = 'block' AND coverage_exclusion_reason = 'm2_calls_missing' WHERE aliquot_barcode = 'GLSS-SM-R110-TP-02D-WXS-BQFEME';
UPDATE analysis.blocklist SET coverage_exclusion = 'block' AND coverage_exclusion_reason = 'm2_calls_missing' WHERE aliquot_barcode = 'TCGA-06-0125-R1-11D-WXS-8Q4RKD';
UPDATE analysis.blocklist SET coverage_exclusion = 'block' AND coverage_exclusion_reason = 'm2_calls_missing' WHERE aliquot_barcode = 'TCGA-06-0125-TP-01D-WXS-Z67AVH';
UPDATE analysis.blocklist SET coverage_exclusion = 'block' AND coverage_exclusion_reason = 'm2_calls_missing' WHERE aliquot_barcode = 'TCGA-06-0152-R1-01D-WXS-MONTUP';
UPDATE analysis.blocklist SET coverage_exclusion = 'block' AND coverage_exclusion_reason = 'm2_calls_missing' WHERE aliquot_barcode = 'TCGA-06-0152-TP-02D-WXS-6DXTU8';
UPDATE analysis.blocklist SET coverage_exclusion = 'block' AND coverage_exclusion_reason = 'm2_calls_missing' WHERE aliquot_barcode = 'TCGA-06-0171-R1-11D-WXS-87WAQK';
UPDATE analysis.blocklist SET coverage_exclusion = 'block' AND coverage_exclusion_reason = 'm2_calls_missing' WHERE aliquot_barcode = 'TCGA-06-0171-TP-02D-WXS-CY280C';
UPDATE analysis.blocklist SET coverage_exclusion = 'block' AND coverage_exclusion_reason = 'm2_calls_missing' WHERE aliquot_barcode = 'TCGA-06-0190-R1-01D-WXS-ODJETQ';
UPDATE analysis.blocklist SET coverage_exclusion = 'block' AND coverage_exclusion_reason = 'm2_calls_missing' WHERE aliquot_barcode = 'TCGA-06-0210-R1-01D-WXS-4MJVD2';
UPDATE analysis.blocklist SET coverage_exclusion = 'block' AND coverage_exclusion_reason = 'm2_calls_missing' WHERE aliquot_barcode = 'TCGA-06-0211-R1-02D-WXS-X1GNKU';
UPDATE analysis.blocklist SET coverage_exclusion = 'block' AND coverage_exclusion_reason = 'm2_calls_missing' WHERE aliquot_barcode = 'TCGA-06-0211-R1-03D-WXS-M22HJ0';
UPDATE analysis.blocklist SET coverage_exclusion = 'block' AND coverage_exclusion_reason = 'm2_calls_missing' WHERE aliquot_barcode = 'TCGA-06-0211-R2-02D-WXS-KTDRP8';
UPDATE analysis.blocklist SET coverage_exclusion = 'block' AND coverage_exclusion_reason = 'm2_calls_missing' WHERE aliquot_barcode = 'TCGA-06-0211-TP-01D-WXS-AS2XJL';
UPDATE analysis.blocklist SET coverage_exclusion = 'block' AND coverage_exclusion_reason = 'm2_calls_missing' WHERE aliquot_barcode = 'TCGA-06-0221-R1-11D-WXS-UAUEGN';
UPDATE analysis.blocklist SET coverage_exclusion = 'block' AND coverage_exclusion_reason = 'm2_calls_missing' WHERE aliquot_barcode = 'TCGA-06-0221-TP-01D-WXS-9K3HSY';
UPDATE analysis.blocklist SET coverage_exclusion = 'block' AND coverage_exclusion_reason = 'm2_calls_missing' WHERE aliquot_barcode = 'TCGA-14-1402-R1-01D-WXS-QGNTYA';
UPDATE analysis.blocklist SET coverage_exclusion = 'block' AND coverage_exclusion_reason = 'm2_calls_missing' WHERE aliquot_barcode = 'TCGA-19-0957-TP-01D-WXS-H59SRY';
UPDATE analysis.blocklist SET coverage_exclusion = 'block' AND coverage_exclusion_reason = 'm2_calls_missing' WHERE aliquot_barcode = 'TCGA-19-1389-R1-21D-WXS-YNQ3L5';
UPDATE analysis.blocklist SET coverage_exclusion = 'block' AND coverage_exclusion_reason = 'm2_calls_missing' WHERE aliquot_barcode = 'TCGA-19-4065-R1-11D-WXS-ET7919';
UPDATE analysis.blocklist SET coverage_exclusion = 'block' AND coverage_exclusion_reason = 'm2_calls_missing' WHERE aliquot_barcode = 'TCGA-19-4065-TP-01D-WXS-FK6Q8U';