About input bam files - Githubissues

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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About input bam files #10

Closed oghzzang closed 4 years ago

oghzzang commented 4 years ago

Dear ERVcaller team,

Hi, I'm Oh.

Thanks for your program.

Then, I have a question.

Can I use GATK pre-processed bam files for input bam of ERVcaller?

I have only pre-processed bam files. In this text, pre-processing means sorting, marking duplicate reads, and recalibrating (https://gatk.broadinstitute.org/hc/en-us/articles/360035535912-Data-pre-processing-for-variant-discovery).

Many Thanks.

Oh.

xunchen85 commented 4 years ago

Hi Oh,

You should be able to use any bam files if it follows the BAM format.

Best, Xun

oghzzang commented 4 years ago

Thanks for your quick reply.

Best,