A program for gathering variant information from a SAM formatted files. SAM_Refiner requires a python interpreter to run. Please report any errors or innacurate outputs so the program may be improved.
$ conda install samrefiner
$ SAM_Refiner -hor for the current, possibly unstable version
$ curl https://raw.githubusercontent.com/degregory/SAM_Refiner/main/SAM_Refiner.py -o SAM_Refiner.py
$ python3 /path/to/SAM_Refiner.py -h$ python SAM_Refiner -r reference.fasta
$ python SAM_Refiner -r reference.gb --wgs 1For information on all current options use:
$ python SAM_Refiner -hSAM Refiner processes SAM formatted files generated from sequencing mapping programs such as Bowtie2 or MiniMap2 to collect variant information relative to a reference sequence and remove chimeric sequences. For details on the original processing and outputs, please refer to the manuscript. If you use SAM Refiner for any published work, please cite Gregory, DA. et al..
2022-04-19 Overhaul of some of the code logic. There should be little effect on usage or output. Usage of .gb ref and specifically --AAcentered is cleaner. Processing for some SAM files will be improved.
2022-04-03 Added insertion reporting to nt call output. Added amino acid centered outputs for unique seqs and covars when using .gb files for reference (--AAcentered 1). Added a tile based method for calculating abundance for covariants in --wgs mode (more computaitonally intensive, more accurate).
2022-02-12 Improved MNP processing, added --ntcover to place a minumum coverage count for nt call output
2022-01-12 Fixed errors, improved MNP processing, added preliminary function to use gb formatted file as reference (-r)
2021-07-11 Separated --min_abundance1 into --min_count and --min_samp_abund, --min_abundance2 now --min_col_abund
2021-06-28 Added --mp to set number of processes, fixed some memory/open file issues.
2021-06-18 Tweaked Covariant Deconvolution algorithm to handle auto-passed covars by least to greatest covar abundance.
2021-06-17 Added --read function to output the read ID and variants for each SAM read line
2021-06-07 Added AA reporting to indel in seq and covar outputs. Reports AA for inframe indels based on the read for seq and covar outputs. May be inconsistent w/ mismatch reporting if mismatches flank the indel.
2021-06-06 Added handling of non canonical NT calls. Anything other than ATCG- will not be recorded. Changed default --max_dist to 40
Currently working on option to use gb format file for reference. Implemented, but not extensively tested. Simply use -r to point to a gb file. Likely won't work on files without CDS entries.
Mode for whole genome sequencing operable. Enabled with --wgs 1, but not yet extensively tested.
A nt call output for only variant calls operable. Enabled with --ntvar 1, but not yet extensively tested.