Tips and Tricks

Tips and Tricks

• Run only part of a variant calling step

OPTIONAL: If you want to rerun the above analysis with different variant call/filter parameters (i.e skip the read cleaning, alignment and post-alignment steps), you can do it as follows:

NOTE: OPTIONAL

python /nfs/esnitkin/bin_group/pipeline/Github/variant_calling_pipeline/variant_call.py -type PE -readsdir /Path-To-Your/test_readsdir/ -outdir /Path/test_output_core/ -analysis output_prefix -index MRSA_USA_300 -steps varcall,filter,stats -cluster parallel-cluster

• Run the variant calling steps on selected samples provided in filenames.txt. filenames.txt should contain fastq filenames with one single-end filename per line.

python /nfs/esnitkin/bin_group/pipeline/Github/variant_calling_pipeline/variant_call.py -type PE -readsdir /Path-To-Your/test_readsdir/ -outdir /Path/test_output_core/ -analysis output_prefix -index MRSA_USA_300 -steps varcall,filter,stats -cluster parallel-cluster -filenames filenames.txt

• Run core_prep and core steps on selected files

If you decide to exclude some samples from the core snp analysis step (step 3), there is a way to run core_prep and core steps on selected files without running the entire pipeline.

python /nfs/esnitkin/bin_group/pipeline/Github/variant_calling_pipeline/variant_call.py -type PE -readsdir /Path-To-Your/test_readsdir/ -outdir /Path/test_output_core/ -analysis output_prefix -index MRSA_USA_300 -steps core -cluster parallel-cluster -filenames filenames_custom