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zstephens / neat-genreads

NEAT read simulation tools
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Sequencing error rate question for whole genomes. #79

Open Anushi opened 3 years ago

Anushi commented 3 years ago

Hi,

Could you please suggest correct parameters to generate WGS data with only sequencing error rate but no mutation rate? I mean I am trying to generate BAM file without any random mutations added due to mutation model, but still I need mutations from sequencing error rate/model?

I tried this command :

python ~/software/neat-genreads/genReads.py -r ~/software/hg38/Chromosomes/chr22.fa -R 126 -o chr22_test12a --bam --vcf --pe 300 30 --rng 10 --no-fastq -c 30 -M 0 -E 0.10 -e ~/software/neat-genreads/models/errorModel_toy.p

Here, I mention -M 0 and -E 0.10 as I need muations from only sequencing error rate. But the golden VCF file does not have mutations added in. Any suggestions?

Thanks very much.