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Robert Bremel

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Latest activity by Robert Bremel
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    Robert Bremel created a post,

    Can vcf file from mutect2 be used in RNAseq short variant discovery

    Can you please provide a) GATK version used b) Exact GATK commands used c) The entire error log if applicable. Docker gatk:latest The method suggested for RNAseq short variant discovery uses haplot...

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    Robert Bremel commented,

    Perhaps the problem is because  -normal  argument (about #75 in -help) is actually a required input in order to keep one's samples sorted out properly  It is not specified as a "Required Argument" ...

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    Robert Bremel created a post,

    mutect2 vcf header

    The  final three lines in the mutect2 header above the column headers is listed as: ##source=Mutect2##tumor_sample=N31May2020##tumor_sample=T31May2020 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ...

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    Robert Bremel commented,

    Thanks Bhanu,   I suspected it was google, but couldn't decipher the output.   I split the input vcf into chromosome subfiles that get done quicker and I got it through the lot.  

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    Robert Bremel commented,

    #5094 suggests processes that run a long time could be an issue?  I am running from a rural area with DSL with only a 5mB/sec download speed.  Might that be an issue causing it to take so long?

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    Robert Bremel commented,

    Tried to re-run the file   Same problem, error in different place this time....     04:56:57.259 ERROR GencodeFuncotationFactory - Problem creating a GencodeFuncotation on transcript ENST0000054553...

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    Robert Bremel created a post,

    Funcotator Appears to have completed but with RunTimeException

    Can you please provide a) GATK version used  Docker 4.1.7.0b) Exact GATK commands used Funcotator -R mydata/refs/Homo_sapiens_assembly19.fasta -V mydata/P62820/analysis/P62820_mutect2_filtered.vcf ...

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    Robert Bremel created a post,

    How is tumor_f in Funcotator MAF

    Can you please provide a) GATK version used b) Exact GATK commands used c) The entire error log if applicable. Using most recent GATK docker. tumor_f is not one of the columns in the MAF specificat...

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    Robert Bremel commented,

    ValidateSamFile is generating the same  warning with 4.1.7.0 Docker version.  How can it be fixed?  Should it be?    It also generates an error   MISSING_PLATFORM_VALUE:Read name A, A platform (PL)...

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    Robert Bremel commented,

    It would be good to point out that the fastq --> bam needs to include the read group tags because they are needed at the recalibrate base quality scores stage of the process and later