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Saloni Sinha

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Latest activity by Saloni Sinha
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    Saloni Sinha commented,

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    3. Error in GATK CollectAllelicCounts

    I did try rerunning one of the failed sample with --read-validation-stringency SILENT, but it gives same error.

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    Saloni Sinha commented,

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    3. Error in GATK CollectAllelicCounts

    I am told that we use ABRA for post processing of the bam files. Otherwise we use bwa and GATK.

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    Saloni Sinha created a post,

    Error in GATK CollectAllelicCounts

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    REQUIRED for all errors and issues: a) GATK version used: gatk-4.3.0.0b) Exact command used: gatk  --java-options -Xmx25g CollectAllelicCounts  -R hs37d5.fa -I X.bam --max-depth-per-sample 30 --min...

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