Simulate SNPs only without indels

[aaronkwc]

Hi.

I wonder if neat-genreads can simulate SNPs only and not do indels when using -M ? I tried using the pickle file from genReads1/models/mutModel_allSNP.p but it gave me the following error:

Traceback (most recent call last): File "/home/aaronkwc/neat-genreads/genReads.py", line 154, in <module> MUT_MODEL = parseInputMutationModel(MUT_MODEL,1) File "/home/aaronkwc/neat-genreads/py/SequenceContainer.py", line 841, in parseInputMutationModel outModel[0] = pickle_dict['AVG_MUT_RATE'] TypeError: list indices must be integers, not str

command used: python ~/neat-genreads/genReads.py \ -r hg19.fasta \ -R 126 \ -c 300 \ -o sim_bamv3/test \ -v mutations.vcf \ -M 0.1 \ -m mutModel_allSNP.p \ -E 0.05 \ --bam \ --vcf \ --pe 300 30 \ --no-fastq

It worked perfectly fine without -m, but I did not want the random indels. Is there anything wrong with the options used? If not, are there any workarounds for this feature? Thanks a lot!!

[zstephens]

Greetings, I added a new mutation model to the repository which has an indel frequency of 0%

models/MutModel_NA12878_noIndel.p

Hope this helps!