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GATK/BWA加速神器Sentieon_202010更新内容

GATK/BWA加速神器Sentieon_202010更新内容

作者: chSNP | 来源:发表于2020-12-04 11:33 被阅读0次
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    Sentieon最新推送版本为V2020,新版本对TNhaplotyper2模块进行了重大更新,使其能匹配4.1.9版本的Mutect2的结果,并引入了三种新算法:ContaminationModel、OrientationBias和TNfilter。在本版中,已经移除tnhaplfilter。具体更新内容如下:

    新添加的功能

    Reduced memory usage when outputting CRAM files.
    Maintenance update of the TNseq algorithm.
    Added DNBSEQ platform to support BGI sequencers.
    Improve speed of umi consensus when not outputting BI/BD tags.
    Added support of BGZF compressed interval list files as well as VCF and VCF.gz files.
    Modified the type of the AD, QSS and RPA FORMAT field in the VCF.
    Override unlimited stack size limit in Linux to prevent Linux bug with thread local storage allocation.
    Using an empty interval bed file will result in no processing done, as if the interval had 0 length.

    Bug修复

    Added additional error checks and error reporting.
    Solved issue that would cause a crash when using BAM files containing reads without a sequence.
    Added option in util sort to handle supplementary reads after processing with the umi tools.
    Solved issue in umi consensus that could cause results to depend on the number of threads.
    Solved issue in Haplotyper that could cause an out of bound memory access error in very rare circumstances
    Solved issue in util sort that could cause it to hang for single threaded jobs under very rare circumstances.
    Solved issue in umi consensus that could cause a segmentation fault.
    Solved issue in umi consensus that produced a non-informative group 0 histogram when using --min_reads 1.

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