Webleanote, Leanote, Not Just A Notepad! 对不起, 该帐户已过期, 博客已停止使用. 如果您是该博客的作者, 请升级您的帐户: 立即升级 WebFeb 12, 2024 · 1) GATK4 validateSam returns some errors to the validation report: The BAM for ValidateSam was generated following the GATK post-processing steps in the order: MarkDuplicates, SortSam, BaseRecalibrator, LeftAlignIndels,FixMateInformation and SetNmMdAndUqTags. a) GATK version used: gatk-4.1.9.0. b) Exact command used:
一个全基因组重测序分析实战 - xiaojikuaipao - 博客园
http://cncbi.github.io/Picard-Manual-CN/command-line-overview.html WebOct 14, 2024 · 3)FixMateInformation. 这一步骤在网上搜到了这个。。。(看来我得好好理出一个现在使用的流程来,生物信息的流程发展还真是快呀!)在一些老版本的pipeline … brittney griner deserves cash
National Center for Biotechnology Information
WebIt looks like there is a problem with the mates in your file and FixMateInformation might not be able to fix it. You could have lost the mates at one point in your analysis by subsetting a file by intervals or downsampling with a tool that was not mate aware. If so, you should go back and fix these steps. This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list. See more Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above. See more When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this … See more If true, assume that the input file is queryname sorted, even if the header says otherwise. boolean false See more If true, ignore missing mates, otherwise will throw an exception when missing mates are found. Boolean true See more WebJun 8, 2024 · I am trying to perform variant calling on a BAM file generated through STAR version STAR_2.6.0b for wheat genome using GATK haplotypecaller as follows: gatk HaplotypeCaller -I sorted.bam -R wheat.... captchaimagecreatecontroller