Running the run_calls wrapper with different numbers of samples produces different SNPs

Hi Zam,

I have three bacterial samples that I want to use to look for SNPs against an assembled reference. To do this, I have tried two methods using the run_calls wrapper. The first was to run each sample against the reference individually. The second, was to run all three samples together against the reference.

The command I used was:

/path/to/CORTEX_release_v1.0.5.17/scripts/calling/run_calls.pl --first_kmer 31 --fastaq_index /path/to/index --auto_cleaning yes --bc yes --pd no --outdir output --outvcf outputvcf --ploidy 1 --stampy_hash stampy_refhash --stampy_bin /path/to/stampy-1.0.31/stampy.py --list_ref_fasta list_ref_fasta --refbindir /path/to/working_directory --genome_size 2800000 --qthresh 5 --mem_height 17 --mem_width 1000 --vcftools_dir /path/to/vcftools_0.1.11 --do_union yes --ref CoordinatesOnly --workflow joint --logfile logfile_output log_1.txt

When I compared the two methods using the 'wk_flow_J_RefCO_FINALcombined_BC_calls_at_all_k.decomp.vcf' I was expecting to see the same SNPs/positions called for each sample, regardless of the method used, however this was not the case. The only difference between the two methods was the index files used:

For running samples individually (e.g. for sample 1):

cat index sample1 . /path /to/sample1_R1 /path /to/sample1_R2

For running samples together:

cat index sample1 . /path /to/sample1_R1 /path /to/sample1_R2 sample2 . /path /to/sample2_R1 /path /to/sample2_R2 sample3 . /path /to/sample3_R1 /path /to/sample3_R2

Am I doing something wrong?

Thanks

iqbal-lab / cortex

Running the run_calls wrapper with different numbers of samples produces different SNPs #17