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collaborativebioinformatics / STRdust

MIT License
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Create simulated STRs #1

Closed wdecoster closed 3 years ago

wdecoster commented 3 years ago

Depends on https://github.com/collaborativebioinformatics/STR_Integration/issues/2

DamarisLa commented 3 years ago

what would be important is to a: sort the bed-file. And tell me how the indexing works in that bedfile. STRsimulator has two or four lines that need to be adjusted as I had bedfiles that started +1 based ending 0 based. And bedfiles starting 0 based and ending 0 based.

DamarisLa commented 3 years ago

python ./simulator7.3.py "REFERENCE.fa" "./manipulated/OUTPUT.fa" "../bedfiles/SORTED_INPUT.bed" "./manipulated/OUTPUT.bed" 0.50 "d" 0.01 10 0.30

Explanation of this example: 0.50 numbers of given regions that should be manipulated "d" for diploid changes : else "h" 0.01 => 1% SNV-mutations added to the STR-regions 10 => 10x rarer is a insertion or deletions (compared to the mutations) 0.30 => 30% homozygous regions rest is heterozygous change to STR-regions

lfpaulin commented 3 years ago

Pipeline is ready, need to be made available in github