Reference Code backup Executable files
Calculate the distributions of deletions across reads
deletion_profile.py -i sample.bam -l 101 -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 |