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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

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The help message of ERVcaller_v1.4.pl

zhutao1009 opened this issue · comments

commented

After I typed the command $perl ERVcaller_v1.4.pl, I got the help message and examples, but I found the examples is conflicting with User Manual of ERVcaller v1.4
The help message is as follows:
perl ./ERVcaller_v1.4.pl

Examples for detecting ERV and other TE insertions:

Detecting TE insertions with a BAM file as the input

   perl /vol6/home/quluj/zt/software/ERVcaller_v1.4/ERVcaller_v1.4.pl -i TE_seq.fa -f .bam -H hg38.fa -T TE_consensus.fa -I folder_of_input_data -O folder_for_output_files -t 12 -S 20 -BWA_MEM

Detecting TE insertions with paired-end FASTQ file as the input

   perl /vol6/home/quluj/zt/software/ERVcaller_v1.4/ERVcaller_v1.4.pl -i TE_seq.fa -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

Detecting TE insertions with separated BAM file(s) as the input

   perl /vol6/home/quluj/zt/software/ERVcaller_v1.4/ERVcaller_v1.4.pl -i TE_seq.fa -f .list -H hg38.fa -T TE_consensus.fa -I folder_of_input_data -O folder_for_output_files -t 12 -S 20 -BWA_MEM -m

Detecting and genotyping TE insertions with a BAM file as the input

   perl /vol6/home/quluj/zt/software/ERVcaller_v1.4/ERVcaller_v1.4.pl -i TE_seq.fa -f .bam -H hg38.fa -T TE_consensus.fa -I folder_of_input_data -O folder_for_output_files -t 12 -S 20 -BWA_MEM -G
commented

Can you help to point out the inconsistency with the following ERVcaller_v1.4 user manual? Thanks!

$ perl user_installed_path/ERVcaller_v1.4.pl -i sample_ID -f .bam -H hg38.fa -T TE_consensus.fa –S 20 -BWA_MEM –t threads

3.3.1 Detecting TE insertions using a BAM file as input
$ perl user_installed_path/ERVcaller_v.1.4.pl -i TE_seq -f .bam -H hg38.fa -T TE_consensus.fa -I folder_of_input_data -O folder_for_output_files -t 12 -S 20 -BWA_MEM

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

3.3.3 Detecting TE insertions using multiple BAM files as input
$ perl user_installed_path/ERVcaller_v.1.4.pl -i TE_seq -f .list -H hg38.fa -T TE_consensus.fa -I folder_of_input_data -O folder_for_output_files -t 12 -S 20 -BWA_MEM -m

3.3.4 Detecting and genotyping TE insertions using a BAM file as input
$ perl user_installed_path/ERVcaller_v.1.4.pl -i TE_seq -f .bam -H hg38.fa -T TE_consensus.fa -I folder_of_input_data -O folder_for_output_files -t 12 -S 20 -BWA_MEM -G

commented

-i TEseq, it should be -i Sample_name

commented

Sorry for the confusion, the "TE_seq" is used as the name of the example input data with the ERVcaller_v1.4.

I have corrected the "TE_seq.fa" in the ERVcaller_v1.4.pl main script.