Add mobile element detection

[J35P312]

Hello there!

I want to add mobile element detection using retroseq (https://github.com/tk2/RetroSeq). Retroseq produces a vcf file, and is run in two steps, discovery, and calling:

1:discovery perl retroseq.pl -discover -bam input.bam -refTEs repeatElement.tab -output output.bed

input.bam is an indexed bam file

repeatElement.tab is a tab separated list, specifying the name of repeats and the genomic position of those repeats. The genomic position is found using the repeat masker tool, I can give you such files on request!

output.bed -output bed file, this is the input of the calling process

2: calling

perl retroseq.pl -call -bam input.bam -input output.bed -ref ref.fasta -output output.vcf -soft

input.bam - indexed bam output.bed - the bed file produced by retroseq discover ref.fasta - reference fasta file, should match the bam file and repeatmasker file output.bed - final output bed

The output vcf should be frequency annotated, I use the following SVDB command:

svdb --query --db SweGen_RetroSeq.vcf --query_vcf retroseq.vcf --bnd_distance 200 --overlap -1

After frequency annotation, I perform gene annotation using VEP (same command as for SV).

I would remove/rank SV based on the FL Format column entry: all variants having an FL of less than 6 should be filtered.

Good luck, and feel free to ask if you have any questions!

[henrikstranneheim]

The repeat mask files would be great both for 37 and 38

[J35P312]

Do you have any server were I can upload it? Or is it ok to put it on KI box for now?

[henrikstranneheim]

If it is not too big you can put it here: https://github.com/Clinical-Genomics/reference-files/tree/master/rare-disease/region via a pull request

[mayabrandi]

Im interested in looking in to this at some point.

[dnil]

• Tested successfully on hasta! Works on ref samples and finds known pathologic event.
• Needs bedtools, samtools and exonerate in PATH.
• Professes to want samtools <=0.1.19, but works with modern versions (e.g. 1.9) after changing the version test in the perl script.
• Needs a simple list of the reference bed files, like so:

  cat retroseq_refs.tab 
  Alu /home/daniel.nilsson/sandbox/reference-files/rare-disease/region/grch37_Alu.bed
  L1  /home/daniel.nilsson/sandbox/reference-files/rare-disease/region/grch37_L1.bed
  SVA /home/daniel.nilsson/sandbox/reference-files/rare-disease/region/grch37_SVA.bed
  HERV    /home/daniel.nilsson/sandbox/reference-files/rare-disease/region/grch37_HERV.bed

[jemten]

Status:

• [ ] Install
• [x] Command module #1419
• [ ] Recipe

[henrikstranneheim]

Should be a project and should not be done in MIP, but in https://github.com/nf-core/raredisease