Closed fpbarthel closed 5 years ago
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)
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.
Done
GLSS-MD-0027
andGLSS-MD-0095
are the same patient.GLSS-MD-0095
>>GLSS-MD-0027
GLSS-MD-0095
sample and caseAffected aliquots:
To-Do:
biospecimen.aliquots
table to change barcodesMD-0095
fromclinical.cases
andclinical.samples
samtools view -H OLDBAM | sed -e 's/SM:OLDBARCODE/SM:NEWBARCODE/' | samtools reheader - OLDBAM > NEWBAM
analysis.files
table to updatealigned BAM
file records to match updated file name and path, new file size and md5biospecimen.readgroups
table to correctSM
tag