zstephens
commented
7 years ago Greetings,
When given a bed file of targeted regions, by default NEAT will sample a majority of the reads from that region, and a fraction of reads from outside the region. This is controlled by the input parameter “-to”, which is 0.02 by default (meaning regions outside the specified regions will be sampled from with probability 2%). By setting -to 0.0 you should able to restrict read sampling to entirely within targeted regions.
Hope this helps! Zach
On Dec 30, 2016, at 3:24 PM, baohua100 notifications@github.com<mailto:notifications@github.com> wrote:
python genReads.py -r hg19.fa -R 150 -c 3000 -t target.bed -o sim1_norm --bam --vcf --pe 350 30
The program still trying to sampling all reads from the genome, but not limited to the target.bed regions.
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python genReads.py -r hg19.fa -R 150 -c 3000 -t target.bed -o sim1_norm --bam --vcf --pe 350 30
The program was still trying to sample all reads from the genome, but not limited to the target.bed regions.