joshfactorial
commented
2 years ago Okay, I've been doing some investigation into this. A couple of things I'm noticing:
- My targeted bed file has only chr1 in it, whereas my input vcf has variants from chr1 and chr2. The variants from chr1 in my input vcf get inserted (whether they are within the targeted region or not), but the variant from chr2 are not inserted.
- force-coverage, for me, slightly increases the coverage, but does not, as the help command claims "force coverage to be constant." Either way, coverage tails off at the ends of reads the region (this is probably due to how NEAT generates the reads)
- I get coverage outside of the targeted regions, even while using "discard-offtarget", in regions, for example, in between the targeted regions (e.g., bed = chr1 0 100, chr1 250 350 results in coverage in the region 100-250, regardless).
I did not see coverage jumping to 20-50x my input coverage. With a -c 25, I saw a max of 30. To my way of thinking, we would want the following behavior:
- insert all valid input variants (i.e., we would still skip variants that had an incorrect REF or whose position was out of range), regardless of targeted bed
- force-coverage produces a constant coverage set of reads
- no reads outside the targeted coverage bed, if --discard-offtarget set
Items 2 and 3 will probably have to wait for version 4.0, because I'm not sure the code will allow for it as written. Item 1 I can work on now. Would you agree with those points?
Hello dev, I have been using your tool to work on some indel simulation and i see that the -c parameter is a hit or miss when it comes to simulation.
Commands that i tried
python ./NEAT/gen_reads.py -r hs37d5.fa -tr target.bed -R 151 -c 25 -E 0.0027 -M 0 -v dup_50_100_NGS120.vcf --pe 255 84 -p 2 --bam --vcf -o neat-50-100-dup-NGS120
so in this case i get coverage around 25 but it drops lower than 25 coverage and doesnt generate the variants that i have provided in the vcf file.
In order to force the coverage i used the --force-coverage parameter shown in the help document --force-coverage [debug] ignore fancy models, force coverage to be constant (default: False)
python ./NEAT/gen_reads.py -r hs37d5.fa -tr target.bed -R 151 -c 25 --force-coverage -E 0.0027 -M 0 -v dup_50_100_NGS120.vcf --pe 255 84 -p 2 --bam --vcf -o neat-50-100-dup-NGS120
after using this command i get the variants i want generated nicely but the coverage in some regions just jump 20-50times more which is also not helpful as the coverage is going way above the required value i want to test at.
Is there a way to get the coverage at a certain level containing the variant with good reads.