Reference Code backup Executable files
Calculate the distribution of mismatches across reads.
mismatch_profile.py -l 101 -i ../test.bam -o out
| --version | show program’s version number and exit |
| -h, --help | show this help message and exit |
| -i INPUT_BAM, --input=INPUT_BAM | |
| Input BAM file. [required] | |
| -l READ_ALIGNMENT_LENGTH, --read-align-length=READ_ALIGNMENT_LENGTH | |
| Alignment length of read. It is usually set to the orignial read length. For example, all these cigar strings (“101M”, “68M140N33M”, “53M1D48M”) suggest the read alignment length is 101. [required] | |
| -o OUTPUT_PREFIX, --out-prefix=OUTPUT_PREFIX | |
| Prefix of output files(s). [required] | |
| -n READ_NUMBER, --read-num=READ_NUMBER | |
| Number of aligned reads with mismatches used to calculate the mismatch profile. default=1000000 | |
| -q MAP_QUAL, --mapq=MAP_QUAL | |
| Minimum mapping quality. default=30 | |