Closed fpbarthel closed 5 years ago
Just to confirm in case you were wondering @roelverhaak, none of the 7 patients to be dropped were used in the paper, whereas the 4 to be kept were.
Also LP03
failed CNV.
CNV-error log error blocklist status
logs/cnv/denoisereadcounts/GLSS-MD-LP03-R1-01D-WGS-4NCFXD.allosomal.log non-neg median fingerprint excl
logs/cnv/denoisereadcounts/GLSS-MD-LP03-R1-01D-WXS-UWJG6Q.allosomal.log non-neg median fingerprint excl
logs/cnv/denoisereadcounts/GLSS-MD-LP03-R1-01D-WXS-UWJG6Q.autosomal.log non-neg median fingerprint excl
logs/cnv/denoisereadcounts/GLSS-MD-LP03-R1-01D-WGS-4NCFXD.autosomal.log non-neg median fingerprint excl
Seven samples had all aliquots marked depricated
UPDATE analysis.files
SET file_format = 'aligned BAM (depricated)'
FROM (SELECT al.aliquot_barcode
FROM biospecimen.samples s
RIGHT JOIN biospecimen.aliquots al ON s.sample_barcode = al.sample_barcode
RIGHT JOIN analysis.files f ON f.aliquot_barcode = al.aliquot_barcode
WHERE case_barcode IN ('GLSS-MD-LP03', 'GLSS-MD-LP07', 'GLSS-MD-LP08', 'GLSS-MD-0019', 'GLSS-MD-0084', 'GLSS-MD-0085', 'GLSS-MD-0137') AND file_format = 'aligned BAM') subq
WHERE files.aliquot_barcode = subq.aliquot_barcode AND file_format = 'aligned BAM'
Four samples had WGS bams (but not WXS) marked depricated
UPDATE analysis.files
SET file_format = 'aligned BAM (depricated)'
FROM (SELECT al.aliquot_barcode, file_format
FROM biospecimen.samples s
RIGHT JOIN biospecimen.aliquots al ON s.sample_barcode = al.sample_barcode
RIGHT JOIN analysis.files f ON f.aliquot_barcode = al.aliquot_barcode
WHERE case_barcode IN ('GLSS-MD-LP01','GLSS-MD-LP02','GLSS-MD-LP04', 'GLSS-MD-LP10') AND file_format = 'aligned BAM' AND aliquot_analysis_type = 'WGS') subq
WHERE files.aliquot_barcode = subq.aliquot_barcode AND file_format = 'aligned BAM'
Update: made a spelling correction, depricated > deprecated
Relevant aliquots marked as deprecated
Several patients are consistently failing M2 calling. Of note, as you can see in the table below, these patients are also blocklisted to varying degrees.
For many of the above patients the quality is so poor that the data is not usuable. However, for 4/11 patients the patient may be salvageable by dropping some of the faulty data.
@roelverhaak please sign off on the to-do list below
To-Do:
entirelyWe chose to leave the data for now and instead mark as deprecated so they will not be used in any analyses.