davidsun / SAP

A DNA sequence analysing & mutation predicting tool

SAP

A DNA sequence analysing & mutation predicting tool.

How to use

Compile

make

Basic usage

Suppose the reference file name is REFERENCE_INPUT_FILE_NAME (for example, human gene), and INPUT_FILE_NAME contains the reads that needed to be mapped onto the reference.

STEP 1: Transform Fasta format into FDA format.

FastaToFDA REFERENCE_INPUT_FILE_NAME > REFERENCE_FDA.fda

STEP 2: Transform Fastq format into FDQ format.

FastqToFDQ INPUT_FILE_NAME > INPUT_FDQ.fdq

STEP 3: Run SAP Mapper.

Mapper -i INPUT_FDQ.fdq -r REFERENCE_FDA.fda -o RESULT.txt

STEP 4: Run Predictor.

Predictor -i RESULT.txt -o VARIATION.txt -r REFERENCE_FDA.fda

The file VARIATION.txt contains the final result.

Options for SAP Mapper

• -f
  FastMap mode.
  Every read is cut into small pieces, which are mapped onto the reference. Usually, one gap between small piece and reference can be tolerated. When FastMap (-f) is enabled, any gap between small piece and reference will NOT be tolerated, which can greatly accelerate the mapping process, and reduce the coverage of mapping.

• -t THREAD_COUNT
  The number of threads when mapping.

• -H HASH_SIZE
  The size of hash table, which can be any number between 20 and 30.
  The actual size of hash table is 2^HASH_SIZE. Larger size of hash table leads to faster mapping when the size of reference is large.

• -C CUT_COUNT
  The number of pieces that every read will be cut into.
  Each piece of read is looked up in the hash table. Usually, larger number of pieces leads to higher coverage of mapping.

• -G GAP_RATIO
  Maximum gap ratio.
  The maximum percentage of gaps in a single read that can be tolerated by SAP Mapper. The gap ratio is defined as MaxGapLength/ReadLength.

• -i FILE_NAME
  Input file name (the file which contains reads, should be in FDQ format).

• -r FILE_NAME
  Reference file name (the file which contains reference, should be in FDA format).

• -o FILE_NAME
  Output file name.

• -p PIECE_SIZE
  The size of small pieces when mapping.
  Smaller size of pieces leads to slower mapping and higher coverage.

• -h
  Help.

Options for SAP Predictor

• -i FILE_NAME
  Input file name (the output of SAP Mapper).

• -r FILE_NAME
  Reference file name (the file which contains reference, should be in FDA format).

• -o FILE_NAME
  Output file name.

• -Q QUALITY
  Minimum quality to validate a read.

• -m READ_DEPTH
  Mimimum depth of reads to validate a insertion/deletion/SNP.
  Here the depth of reads means the number of reads that covers the location of insertion/deletion/SNP.

• -h
  Help.

Options for SAP SNPFilter

• -i FILE_NAME
  Input file name (the output of SAP Predictor).

• -o FILE_NAME
  Output file name.

• -m READ_DEPTH
  Minimum depth of reads to call a SNP.

• -M READ_DEPTH
  Maximum depth of reads to call a SNP.

• -s SCORE
  Maximum score to call a SNP.
  For the output of SAP Predictor, higher score means lower possiblity that a SAP happens.

• -h
  Help.