├── Database ├── ERV_library.fa ├── HERVK.fa ├── Human_TE_library.fa └── TE_consensus.fa ├── ERVcaller_v1.4.pl ├── README.md ├── Scripts ├── Break_point_calling.pl ├── Calculate_reads_among_nonTE_locations.pl ├── Check_paired_end.pl ├── Combine_VCF_files.pl ├── Distinguish_nonTE_from_missing_genotype.pl ├── EC_filtered1.pl ├── ERV_Assign_reads-filter.pl ├── ERV_Filtered_fastq.pl ├── ERV_Result_visual.pl ├── ERV_filter_reads.pl ├── ERV_get_name.pl ├── ERV_get_reads.pl ├── ERV_organize_reads.pl ├── Extract_fastq.pl ├── Extract_fastq_sf.pl ├── Extract_specific_loci_final_visualization.pl ├── Filtered_ERVcaller_1.pl ├── Filtered_fastq.pl ├── Filtered_integration.pl ├── Filtered_single_reads.pl ├── Filtering_VCF_v1.4.pl ├── Fine_mapped.pl ├── Genotype_likelihood.R ├── Order_by_TE_sequence.pl ├── Reads_summary.pl ├── Remove_redundancy_split_reads.pl ├── Result_filtered.pl ├── Result_finalize3.pl ├── Results_get.pl ├── SE-MEI-master.tar.gz └── Soft_clipping_transfer.pl └── test ├── BWA ├── TE_seq.bam └── TE_seq.bam.bai ├── Bowtie ├── TE_seq_bowtie.bam └── TE_seq_bowtie.bam.bai ├── FASTQ ├── TE_seq2_1.fq.gz ├── TE_seq2_2.fq.gz ├── TE_seq_1.fq.gz └── TE_seq_2.fq.gz ├── Multiple_BAMs ├── TE_Merge.list ├── TE_seq.bam ├── TE_seq.bam.bai ├── TE_seq2.bam └── TE_seq2.bam.bai └── example_output └── TE_seq.vcf /Database/ERV_library.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xunchen85/ERVcaller/HEAD/Database/ERV_library.fa -------------------------------------------------------------------------------- /Database/HERVK.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xunchen85/ERVcaller/HEAD/Database/HERVK.fa -------------------------------------------------------------------------------- /Database/Human_TE_library.fa: -------------------------------------------------------------------------------- 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