Consolidate GLSS-MD-0027 and GLSS-MD-0095

[fpbarthel]

GLSS-MD-0027 and GLSS-MD-0095 are the same patient.

• Recode aliquots from GLSS-MD-0095 >> GLSS-MD-0027
• Get rid of GLSS-MD-0095 sample and case

Affected aliquots:

GLSS-MD-0027-NB-01D-WGS-RVOO5S
GLSS-MD-0027-R1-01D-WGS-88ST4Y
GLSS-MD-0027-R2-01D-WGS-55XI5C
GLSS-MD-0027-TP-01D-WGS-6HFKNZ
GLSS-MD-0095-NB-01D-WXS-7SK6Q5 >> GLSS-MD-0027-NB-01D-WXS-7SK6Q5
GLSS-MD-0095-R1-01D-WXS-HX8R83 >> GLSS-MD-0027-R1-01D-WXS-HX8R83
GLSS-MD-0095-TP-01D-WXS-OAQEYZ >> GLSS-MD-0027-TP-01D-WXS-OAQEYZ

To-Do:

• [x] Update biospecimen.aliquots table to change barcodes
• [x] Remove MD-0095 from clinical.cases and clinical.samples
• [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] Update biospecimen.readgroups table to correct SM tag
• [x] Remove misnamed BAMs
• [x] Copy new data to tier2

[moskalika]

Are these bam files of the same sample? If not the 01D should probably be 02D for the newly converted barcodes

(the current 0027 barcodes have the correct surgery order)

[Kcjohnson]

It turns out we don't know whether these samples represent the same or different DNA extractions(i.e., different portions). If we treat them as -01D- and -02D- this might allow them to be used in downstream analyses for multi-sector studies, when in fact they may not be multi-sector.

I vote that we leave both WGS and WXS as -01D- so that we avoid the "multi-sector or not?" issue.

[fpbarthel]

Done