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 … WebAug 19, 2024 · FixMateInformation (Picard) Verify mate-pair information between mates and fix if needed.This tool ensures that all mate-pair information is in sync between each …
Failed to detect whether we are running on Google Compute
WebJun 13, 2024 · 这里同样包含了两个步骤: 第一步,BaseRecalibrator,这里计算出了所有需要进行重校正的read和特征值,然后把这些信息输出为一份校准表文件(sample_name.recal_data.table) 第二步,PrintReads,这一步利用第一步得到的校准表文件(sample_name.recal_data.table)重新调整原来 ... WebFind changesets by keywords (author, files, the commit message), revision number or hash, or revset expression. sharks ian
2024-04-04 BioData Catalyst Ecosystem Release Notes
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 … Web$ java -jar FixMateInformation.jar INPUT=MO_136.marked.realigned.bam OUTPUT=MO_136.fixed.bam SO=coordinate VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true & Then: [rzeng@qlogin3 reference]$ [Mon Oct 20 10:17:35 EDT 2014] net.sf.picard.sam.FixMateInformation INPUT=[MO_136.marked.realigned.bam] … WebJun 13, 2024 · 5 为什么进行FixMateInformation. Fixmate checks the two mates from a paired-end bam (name sorted) and then updates the flags and insert sizes. IMHO that … sharks hunting seals