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prasundutta87

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Latest activity by prasundutta87
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    prasundutta87 commented,

    Thanks a lot for this, Genevieve-Brandt-she-her! It was really helpful.

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    prasundutta87 commented,

    Hi,I think this is what happened. After visualising a very small exonic portion from hg38, I observed that ApplyBQSR removed reads outside the exonic region. Please see the attached picture. Howeve...

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    prasundutta87 created a post,

    output BAM form ApplyBQSR query using --interval option

    Hi,I am dealing with exome germline variant calling. As per https://gatk.broadinstitute.org/hc/en-us/articles/360035531852-Intervals-and-interval-lists, we should always use --intervals (and --inte...

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    prasundutta87 commented,

    Hi Bhanu, Thanks for your reply. Sorry, I was'nt clear with my question. I was going through some old documents on how to confirm if BQSR has worked well. In most of the documents, a second recalib...

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    prasundutta87 commented,

    Hi, There was a -bqsr option in old version of BaseRecalibrator. In order to produce a second recalibration table, you could give the first recalibration table to it along with the original BAM fil...

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    prasundutta87 created a post,

    Truth set download page for BQSR

    Answered

    If you are seeing an error, please provide(REQUIRED) : a) GATK version used: 4.1.9.0b) Exact command used: BaseRecalibrator and ApplyBQSRc) Entire error log: NoneIf not an error, choose a category ...