Question of setting the -H parameter

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.

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

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Question of setting the -H parameter #31

Open vegetableyu opened 7 months ago

vegetableyu commented 7 months ago

Hi there, I would like to kindly inquire, if I input a BAM file that is aligned to 'GRCh38_full_analysis_set_plus_decoy_hla.fa', when executing 'ERVcaller_v1.4.pl', should the '-H' parameter input be 'GRCh38_full_analysis_set_plus_decoy_hla.fa', or should it still be the 'hg38.fa' without ALT contig? I appreciate your guidance on this matter. Thank you.

xunchen85 commented 6 months ago

Hi,

It would say that it would be better to use the same reference genome as the input BAMs even though it may not change the results.

Best, Xun