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zstephens / neat-genreads

NEAT read simulation tools
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Simulating genomes with complex ploidy #93

Open Militeee opened 3 years ago

Militeee commented 3 years ago

Hi,

My problem is very simple, I'm trying to generate fastq files starting from a given segmentation of the genome (chr, strat, end, minorAll, majorAll). As far as I can see the tool is able to produce only genomes with a fixed ploidy. My idea was to simulate the whole genome starting from the smallest CN and then proceed additively to obtain the final profile. Does it seem sensible or does NEAT allow you to do this automatically?

Thanks.

joshfactorial commented 3 years ago

Greatings! First off, we recommend using the latest repository for NEAT, which is found here: https://github.com/ncsa/NEAT. The latest development will be found there. I do not have direct experience using NEAT this way yet. However, you can use the output vcf from NEAT as input into NEAT, so if you do a targeted mutation using a bed file, you could then use those variants as input. Or you can run small parts of the genome through NEAT, then concatenate the results together. You may have to do some other processing to deal with ploidy. NEAT currently does not do copy number variants.