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Thread: what software do you use for interpretation of Full Genomes Corp results?

  1. #1
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    Post what software do you use for interpretation of Full Genomes Corp results?

    what software do you use for interpretation of Full Genomes Corp results? I can't see nothing from my PC.

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    IGV can be used to manually explore the .bam file. http://www.broadinstitute.org/software/igv/home
    To extract variants and strs you can use Felix Chandrakumar's Bam Analysis kit http://www.y-str.org/2014/04/bam-analysis-kit.html .
    FGC already provides you with the variants and STRs so you shouldn't really have to use the second tool.

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    BAMview is also neat if you want to look at each read rather than have them consolidated. It will create an index (.bai) file for you which IGV needs.

    Also consider uploading to YFull.com who have a good analysis service and a very nice interface. Once its up there you can 'browse' the data easily looking up either SNPs or raw positions without having to load a browser like IGV.

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    I found sometimes at same position, reads from Bamview and IGV is different, what cause this?

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     paulgill (08-29-2015)

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    Are you definitely using the right reference sequence? That's the first thing to check.

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    Even don't use reference sequence with bam view, I still could count the reads

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    So, does FGS give rs numbers for known polymorphisms. Do I have to pay extra $250 for that?

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    Quote Originally Posted by pauleug View Post
    So, does FGS give rs numbers for known polymorphisms. Do I have to pay extra $250 for that?
    The $250 covers the analysis of the genes that have confirmed by the American College of Medical Genetics. Essentially, the purpose of that analysis is to report only the medically relevant (proven results).

    It is a much smaller report than the Promethease or other types. However, the reason for that is that it only focuses on the medically relevant data. It only reports results that have been confirmed by the ACMG.

    Promethease and other services may report results that have not been proven.

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    Anyone get WGS Extract Beta to work with their FGC BAM files? I know my files are good, YFull had no issue with them, but when I try to export either Y-DNA/mtDNA or just Y-DNA or any autosomal stuff from either the hg19 or hg38 bam files, it just puts out like an empty 3KB file.
    Paternal - Y-DNA: J2b2* (J-M241) Z2432+ Z2433+ Y978+ (J2b2a2b1*) (Hidden Content ) (YFull: YF02959) (FTDNA Kit B6225), mtDNA: M18a* (FTDNA Kit 329180) (YFull: YF63773)
    Maternal- Y-DNA: R1a1a1b2a1a2c2d5a* L657+ Y7+ (R-Y16494*) (FTDNA Kit 311047) (YFull: YF68408), mtDNA: Hidden Content (FTDNA Kit B6225) (YFull: YF02959) (Mother's Mother's Father: R1a1a1b2a1a2c2* Y7+ Y29+ (R-Y29*) (FTDNA Kit 329181) (YFull: YF65256))

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    FGC used GRCh37, which doesn't contain the chr prefix on the contigs and doesn't use the Yoruba mtDNA reference. If the software is incorrectly coded it may not be able to deal with the reference.

    As a note if this is a Y Elite BAM, you shouldn't expect to see anything useful in the off-target reads in the autosomal regions.

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