RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements. Please read the wiki page (link below) for usage instructions. Also, there is a page on the wiki describing how the 1000 genomes CEU trio was carried out with the files and parameters used for the various steps.
This pull request enables RetroSeq to handle cram files. This is facilitated by using a modern version of samtools (newer than 1.10) and some changes in the code for checking files (e.g. also allow cram files when looking for cram.) Bam support is still supported.
[feature] Added support for cram files. Requires samtools 1.10 and newer
[speedup] decodes only parts of cram files used by RetroSeq Perl script
[fix] Samtools can not extract regions with a negative start position. Negative values are set to zero. This may occur in HG38 reference with alt contigs
This pull request enables RetroSeq to handle cram files. This is facilitated by using a modern version of samtools (newer than 1.10) and some changes in the code for checking files (e.g. also allow cram files when looking for cram.) Bam support is still supported.