Reference Code backup Executable files
According to SAM specification, if Q is the character to represent “base calling quality” in SAM file, then Phred Quality Score = ord(Q) - 33. Here ord() is python function that returns an integer representing the Unicode code point of the character when the argument is a unicode object, for example, ord(‘a’) returns 97. Phred quality score is widely used to measure “reliability” of base-calling, for example, phred quality score of 20 means there is 1/100 chance that the base-calling is wrong, phred quality score of 30 means there is 1/1000 chance that the base-calling is wrong. In general: Phred quality score = -10xlog(10)P, here P is probability that base-calling is wrong.
read_quality.py -i Pairend_nonStrandSpecific_36mer_Human_hg19.bam -o output
| --version | show program’s version number and exit |
| -h, --help | show this help message and exit |
| -i INPUT_FILE, --input-file=INPUT_FILE | |
| Alignment file in BAM or SAM format. [required] | |
| -o OUTPUT_PREFIX, --out-prefix=OUTPUT_PREFIX | |
| Prefix of output files(s). [required] | |
| -r REDUCE_FOLD, --reduce=REDUCE_FOLD | |
| To avoid making huge vector in R, nucleotide with particular phred score less frequent than this number will be ignored. Increase this number save more memory while reduce precision. Set to 1 achieve maximum precision (i.e. every nucleotide will be considered). This option only applies to the ‘boxplot’. default=1000 | |
| -q MAP_QUAL, --mapq=MAP_QUAL | |
| Minimum mapping quality (phred scaled) for an alignment to be called “uniquely mapped”. default=30 | |