Consolidate MD-LP09/MD-0137 and MD-LP20/MD-0112

[fpbarthel]

It turns out MD-LP09 and MD-0137 are in fact the same patient, as well as MD-LP20 and MD-0112. We now need to consolidate all their data into the same patient barcode.

Affected aliquots:

GLSS-MD-LP09-R1-01D-WGS-2AEXZ1 >> GLSS-MD-0137-R1-01D-WGS-2AEXZ1
GLSS-MD-LP09-TP-01D-WGS-L1K3MT >> GLSS-MD-0137-TP-01D-WGS-L1K3MT 
GLSS-MD-LP09-NB-01D-WGS-C42CZJ >> GLSS-MD-0137-NB-01D-WGS-C42CZJ
GLSS-MD-0137-R1-01D-WXS-GBFAG8
GLSS-MD-0137-TP-01D-WXS-9LXGRU
GLSS-MD-0137-NB-01D-WXS-KOXSFV

GLSS-MD-LP20-R1-01D-WGS-YG70ME >> GLSS-MD-0112-R1-01D-WGS-YG70ME
GLSS-MD-LP20-TP-01D-WGS-WIQ0DD >> GLSS-MD-0112-TP-01D-WGS-WIQ0DD
GLSS-MD-LP20-NB-01D-WGS-CDM1PT >> GLSS-MD-0112-NB-01D-WGS-CDM1PT
GLSS-MD-0112-NB-01D-WXS-Y6PUVW
GLSS-MD-0112-R2-01D-WXS-P1B0I2
GLSS-MD-0112-R1-01D-WXS-GI18JQ

To-Do:

• [x] Update biospecimen.aliquots table to change barcodes
• [x] Remove LP09 and LP20 from clinical.cases
• [x] Rename BAM files using the following command: samtools view -H OLDBAM | sed -e 's/SM:OLDBARCODE/SM:NEWBARCODE/' | samtools reheader - OLDBAM > NEWBAM
• [x] Regenerate bai indices
• [x] Rename BQSR tables
• [x] Regenerate MD5 checksums
• [x] Edit analysis.files table to update aligned BAM file records to match updated file name and path, new file size and md5
• [x] Remove misnamed BAMs
• [x] Copy new data to tier2

[fpbarthel]

Update aliquots:

UPDATE biospecimen.aliquots SET aliquot_barcode = 'GLSS-MD-0137-R1-01D-WGS-2AEXZ1', aliquot_portion = 1, sample_barcode = 'GLSS-MD-0137-R1' WHERE aliquot_barcode = 'GLSS-MD-LP09-R1-01D-WGS-2AEXZ1';
UPDATE biospecimen.aliquots SET aliquot_barcode = 'GLSS-MD-0137-TP-01D-WGS-L1K3MT ', aliquot_portion = 1, sample_barcode = 'GLSS-MD-0137-TP' WHERE aliquot_barcode = 'GLSS-MD-LP09-TP-01D-WGS-L1K3MT';
UPDATE biospecimen.aliquots SET aliquot_barcode = 'GLSS-MD-0137-NB-01D-WGS-C42CZJ', aliquot_portion = 1, sample_barcode = 'GLSS-MD-0137-NB' WHERE aliquot_barcode = 'GLSS-MD-LP09-NB-01D-WGS-C42CZJ';
UPDATE biospecimen.aliquots SET aliquot_barcode = 'GLSS-MD-0112-R1-01D-WGS-YG70ME', aliquot_portion = 1, sample_barcode = 'GLSS-MD-0112-R1' WHERE aliquot_barcode = 'GLSS-MD-LP20-R1-01D-WGS-YG70ME';
UPDATE biospecimen.aliquots SET aliquot_barcode = 'GLSS-MD-0112-TP-01D-WGS-WIQ0DD', aliquot_portion = 1, sample_barcode = 'GLSS-MD-0112-TP' WHERE aliquot_barcode = 'GLSS-MD-LP20-TP-01D-WGS-WIQ0DD';
UPDATE biospecimen.aliquots SET aliquot_barcode = 'GLSS-MD-0112-NB-01D-WGS-CDM1PT', aliquot_portion = 1, sample_barcode = 'GLSS-MD-0112-NB' WHERE aliquot_barcode = 'GLSS-MD-LP20-NB-01D-WGS-CDM1PT';

[fpbarthel]

Turns out that for MD-0112 there is no TP sample and in fact R2 represents the primary.

UPDATE biospecimen.aliquots SET aliquot_barcode = 'GLSS-MD-0112-R2-01D-WGS-WIQ0DD', aliquot_portion = 1, sample_barcode = 'GLSS-MD-0112-R2' WHERE aliquot_barcode = 'GLSS-MD-LP20-TP-01D-WGS-WIQ0DD';

Note: obviously this is a temporary fix and should be fixed later.

[fpbarthel]

Done