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payal banerjee

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Latest activity by payal banerjee
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    payal banerjee commented,

    1. Tool Index
    2. 4.0.5.2
    3. RevertSam (Picard)

    Hello,  I am trying to follow the mitochondrial variant calling pipeline by GATK 4.4.0.0. I want use RevertSAM.  I noticed a couple of options for "ATTRIBUTE_TO_CLEAR" are most probably deprecated....

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    payal banerjee commented,

    1. Community
    2. Other
    3. BaseRecalibrator on MT .bam files

    Thanks Sharon Natasha Cox

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    payal banerjee commented,

    1. Community
    2. Other
    3. BaseRecalibrator on MT .bam files

    Where to download the MITOMAP_HMTDB_known_indels_RCRS.vcf file from?  I see - https://www.mitomap.org/foswiki/bin/view/MITOMAP/Resources https://mitomap.org/cgi-bin/polymorphisms.cgi?format=vcf I...