kircherlab / mpraoligodesign Goto Github PK

Variants which are in the design_variants.variants.vcf.gz or the design_variants.variant_region_map.tsv.gz but not anymore in the _filtered versions of these files remain in the design file.
Example 80K ALT_LMNA|ENSG00000160789.24|EH38E2840374_fwd_tile1-1_LMNA|ENSG00000160789.24|EH38E2840374|1-156033864-A-T

For MPRAsnakeflow or other tools we need an output that does not contain duplications of sequences. They have to be collapsed into one.

Add an option (flag) which outputs the headers of failed sequences and the corresponding reason

or

Add a tag to the fasts header as tag/comment i.e. after a whitespace and implement a filtering step which filters the fasta headers based on their tags in the end and remove the tag section again

For the last approach a concluding list of removed headers and their reason as a table might be useful

Check fasta headers that they

• contain the correct charset of fasta files
• are unique across complete design
• take care of spaces

During the filtering steps regions will be filtered out but their ids remain in the final output vcf file
example for 80K ARV1|ENSG00000173409.14|EH38E2873165_fwd_tile1-1