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  • .bam files

    Thanks for the data in VCF and BED files. Can anybody say when the files will be in .bam format? I have heard it is forthcoming in a few weeks,but would like to confirm this.

  • #2
    BAM files

    Please can we have news on when BAM files will be available as so far the VCF files for M222 indicate a lot of the SNPs we need aren't being reported. Without those we can't begin to make use of the new lower level SNPs. I am hopeful that the raw data will shed more light on the issue.

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    • #3
      Hello,

      If you would like your .BAM file, please contact customer support, [email protected]. You can put BIG Y .BAM request in the subject line.
      Originally posted by ikennedy View Post
      Please can we have news on when BAM files will be available as so far the VCF files for M222 indicate a lot of the SNPs we need aren't being reported. Without those we can't begin to make use of the new lower level SNPs. I am hopeful that the raw data will shed more light on the issue.

      Comment


      • #4
        Thanks. Are you able to quote a typical file size? I know ones from external sources have been about 8Gb.

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        • #5
          I should have updated the thread. I read another post whereby the poster was advised to request the .bam files through customer service. So, I did the same last week and received a response that my .bam file should be here soon. It will come as a link to access, rather than the file being sent to my computer, given its size.

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          • #6
            BAM File Size

            Rebekah,

            What is the average size for the BAM files?

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            • #7
              I received mine a short time ago. It is 1.2GB.

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              • #8
                Originally posted by muso View Post
                I received mine a short time ago. It is 1.2GB.
                How was the file sent to you, as a link or is it on your results page?

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                • #9
                  Originally posted by gerlyons View Post
                  How was the file sent to you, as a link or is it on your results page?
                  A link in my email inbox.

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                  • #10
                    muso, have you viewed it yet? Is that definitely an umcompressed file size? I would have expected it to be >50% of a FGC one but mine was 8Gb.

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                    • #11
                      Originally posted by ikennedy View Post
                      muso, have you viewed it yet? Is that definitely an umcompressed file size? I would have expected it to be >50% of a FGC one but mine was 8Gb.
                      I will be the first to admit that I am not very technically savvy. I have WinZip on my computer and when the download was finished and was in a a zipped file. I did open the file, but I was receiving various commands regarding this, and, to be honest, I am not sure what they meant. More importantly for me, I forwarded the link to YFull for analysis.

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                      • #12
                        Originally posted by muso View Post
                        I will be the first to admit that I am not very technically savvy. I have WinZip on my computer and when the download was finished and was in a a zipped file. I did open the file, but I was receiving various commands regarding this, and, to be honest, I am not sure what they meant. More importantly for me, I forwarded the link to YFull for analysis.
                        OK that sounds like you are quoting the compressed file size - perhaps you can post if and when you uncompress it for its original size? Thanks.

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                        • #13
                          Originally posted by ikennedy View Post
                          OK that sounds like you are quoting the compressed file size - perhaps you can post if and when you uncompress it for its original size? Thanks.
                          A BAM file is a compressed format. The size of the file will not really be much different than the size of the downloaded ZIP file. Zipping a BAM file really does not make much sense.

                          The BIG-Y BAM file that I currently have access to has a size of 2.2GB.

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                          • #14
                            Originally posted by wkauffman View Post
                            A BAM file is a compressed format. The size of the file will not really be much different than the size of the downloaded ZIP file. Zipping a BAM file really does not make much sense.

                            The BIG-Y BAM file that I currently have access to has a size of 2.2GB.
                            If I may, what program are you using to open the file?

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                            • #15
                              You use Samtools to convert a .bam to a .sam file.

                              The .sam file is human readable, and can also be read in Excel ... but likely is far too big to read in one hunk.
                              This is passably user friendly.

                              Samtools is a Linux program but there is a Windows port that
                              partially works, and this part does, as does
                              the creation of Pileup files, which are much nicer
                              to look at. However, that requires downloading other files too. This is not user friendly.

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