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manolis

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Latest activity by manolis
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    manolis commented,

    Many thanks Genevieve Brandt and David Benjamin

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    manolis created a post,

    Mutect2 multi-sample pipeline

    Can you please provide a) GATK version used GATK 4170b) Exact GATK commands used c) The entire error log if applicable.   Hi GATK team, I have 2 tumor samples and 1 normal sample, all for the same ...

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    manolis commented,

    Hi Bhanu Gandham, I'm waiting for it in the future :) Thanks!    

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    manolis commented,

    Many thanks David Benjamin!

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    manolis commented,

    Thank you very much Bhanu Gandham, I will try the last version. Best  

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    manolis commented,

    Hi, I tested one of the 3 failed sample with the 4.1.3.0 version and I do not have any erro, related to my initial post.

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    manolis created a post,

    gCNV; CollectSampleQualityMetrics; maximum_number_events_per_sample

    Can you please provide a) GATK version used v4.1.6.0b) Exact GATK commands used c) The entire error log if applicable.   Hi, about gCNV pipeline with 102 WES data (no chrY, padding 100bp, average c...

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    manolis commented,

    I add a more general question: you advice to use in a pipeline the same tool version, for example when I go to use the Mutect2-TumorOnly pipeline I have to pre-process+PoN+Mutect2+downsteam somatic...

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    manolis commented,

    I tested some WES and works. I also tested 4 WGS and for only one works, the other 3 have the same problem. For the WGS that does not work I have an output file (.vcg.gz, .tbi), of smaller sizes, a...

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    manolis created a post,

    PoN: Mutect2 error

    Can you please provide a) GATK version used 4.1.6.0b) Exact GATK commands used ${GATK4} Mutect2 \-R ${hg38} \-I ${bam} \-O ${samplePON} \-L ${INTERVAL} \-ip ${ipM2} \--max-mnp-distance 0 \--tmp-dir...