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Laurent MANCHON

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Latest activity by Laurent MANCHON
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    Laurent MANCHON commented,

    yes, i known.But it works fine with past version of GATK, so, my solution was to use version 4.2.6.1 with R-3.6.2

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    Laurent MANCHON created a post,

    problem with R library

    REQUIRED for all errors and issues: a) GATK version used:4.4b) Exact command used: module load Python-3.11.1 java.17.0.6module load R.4.3.0 # with getopt_1.20.0 and optparse_1.3.2 gatk --java-optio...

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    Laurent MANCHON commented,

    for now this problem is over for me because i have added those parameters to Mutect2: --read-filter NotSecondaryAlignmentReadFilter \--read-filter NotSupplementaryAlignmentReadFilter \--interval-pa...

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    Laurent MANCHON commented,

    no.this is the command i use: bwa-mem2 mem -M -w 150 -d 80 -c 2000 -t 24 -R "@RG\tID:${lib}\tSM:${lib}\tLB:${lib}\tPL:ILLUMINA" $GENOME/GRCh38_p13.fa $f1 $f2 | samtools fixmate -O bam -@ 24 - - | s...

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    Laurent MANCHON commented,

    i have only a tumor bam file and a pon.hdf5 and no normal libraryIs it possible to use this pipeline ?I'm looking for a bash pipeline with all the GATK commands to find the CNV, is it available som...

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    Laurent MANCHON commented,

    that's what I did in my analysis, I used the genome GRCh38_p13 (08.2022) from gencode consortium. I have removed all the alts contigs and use only the chromosome sequences.  

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    Laurent MANCHON commented,

    from Mutect2 vcf output: zcat HD_829_Mutect2.vcf.gz | grep "chr17" | grep "7669692"chr17   7669692 .       T       G       .       .       AS_SB_TABLE=340,402|25,36;DP=817;ECNT=1;MBQ=20,20;MFRL=236...

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    Laurent MANCHON created a post,

    splice variants are missing from the Mutect2 output

    REQUIRED for all errors and issues: a) GATK version used: gatk-4.2.6.1 b) Exact command used: gatk --java-options "-Xms128G -Xmx128G -XX:-UseGCOverheadLimit -XX:+UseParallelGC -XX:ParallelGCThreads...

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    Laurent MANCHON created a post,

    How to recover a mutation from secondary alignment

    REQUIRED for all errors and issues: a) GATK version used: gatk-4.2.6.1b) Exact command used:  gatk --java-options "-Xms80G -Xmx80G -XX:-UseGCOverheadLimit -XX:+UseParallelGC -XX:ParallelGCThreads=1...

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    Laurent MANCHON created a post,

    base recalibration

    REQUIRED for all errors and issues: a) GATK version used: b) Exact command used: c) Entire program log: gatk --java-options "-Xms64G -Xmx64G -XX:-UseGCOverheadLimit -XX:+UseParallelGC -XX:Parallel...