Giters

xunchen85 / ERVcaller

ERVcaller is a tool designed to accurately detect and genotype non-reference unfixed endogenous retroviruses (ERVs) and other transposable elements (TEs) in the human genome using next-generation sequencing (NGS) data. We evaluated the tools using both simulated and real benchmark whole-genome sequencing (WGS) datasets. ERVcaller is capable to accurately detect various TE insertions of any lengths, particularly ERVs. It allows for the use of a TE reference library regardless of sequence complexity, such as the entire RepBase database. It is easy to install and use with command lines.

Home Page:http://www.uvm.edu/genomics/software/ERVcaller.html

Geek Repo:Geek Repo

Github PK Tool:Github PK Tool

Error in User Manual

zhutao1009 opened this issue · comments

commented

The original text is as follows：
3.3.2 Detecting TE insertions using paired-end FASTQ file as input
$ perl user_installed_path/ERVcaller_v.1.4.pl -i TE_seq -f .fq.gz -H hg38.fa -T TE_consensus.fa -I folder_of_input_data -O folder_for_output_files -t 12 -S 20 -BWA_MEM
如果使用了-BWA_MEM 参数会导致程序把输入文件当成bam文件，需要去掉-BWA_MEM程序才能正常运行

commented

it make sense, -BWA_MEM is a parameter for the use of BAM files as the input. The help page of ERVcaller_v1.4.pl script is corrected. I will corrected the corresponding sentence in the manual.