[DOCKTESTERS] Summary of validation of Dockers Sanger and DKFZ(+Delly)

[Miguel Vazquez]

Junjun,

The section to refer about preparing the unaligned version of the BAM seems
the same as when I first went through it. The command-line featured there
reads

cat initial.bam | bamreset exclude=QCFAIL,SECONDARY,SUPPLEMENTARY
resetheadertext=header.sam md5=1 md5filename=cleaned.bam.md5 > cleaned.bam

Since some of the options refer to setting the header and performing the
md5 etc, I've stripped it down to:

cat initial.bam | bamreset exclude=QCFAIL,SECONDARY,SUPPLEMENTARY >
cleaned.bam

Do you think there is any reason that this might not work? I don't see how
the header info would have any effect on the process. I would be good to
rule this out as a source of the problem.

Best

Miguel



On Mon, Jan 16, 2017 at 4:24 PM, Junjun Zhang <Junjun.Zhang at oicr.on.ca>
wrote:

> Hi,
>
> I’d like to point out that this wiki page is obsolete: https://wiki.oicr.
> on.ca/display/PANCANCER/Preparing+paired-end+data+for+upload.
>
> It has been replaced by the FINAL SOP for preparing PCAWG sequences here:
> https://wiki.oicr.on.ca/display/PANCANCER/PCAWG+%28a.
> k.a.+PCAP+or+PAWG%29+Sequence+Submission+SOP+-+v1.0. Many of us worked on
> it including Keiran.
>
> Regarding preparation of test input BAM from merged / aligned BAM, the
> first step (*Your starting files must be for a single lane of
> sequencing in either BAM (unaligned BAM) or FASTQ*) of this section is
> most relevant: https://wiki.oicr.on.ca/display/PANCANCER/PCAWG+
> %28a.k.a.+PCAP+or+PAWG%29+Sequence+Submission+SOP+-+v1.
> 0#PCAWG(a.k.a.PCAPorPAWG)SequenceSubmissionSOP-v1.0-5.
> Prepareyoursequencefiles
> <https://wiki.oicr.on.ca/display/PANCANCER/PCAWG+%28a.k.a.+PCAP+or+PAWG%29+Sequence+Submission+SOP+-+v1.0#PCAWG%28a.k.a.PCAPorPAWG%29SequenceSubmissionSOP-v1.0-5.Prepareyoursequencefiles>
>
> Hope this helps,
>
> Junjun
>
>
>
> *Junjun Zhang*
>
>
> Lead bioinformatician
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