Add Missing Quality Score to Bam FIle. Some mappers, e.g. LRA will generate bam file with some alignments's quality scores missed. Here I wrote a python scipt to restore those quality scores from the original fastq file. The quality scores are important information for SNPs and SV calling.
usage: python addQuality.py [-h] [-i IN_BAM] [-o OUT_SAM] [-f FASTQ]
Add missing query qualities to bam file
optional arguments: -h, --help show this help message and exit -i IN_BAM, --in_bam IN_BAM input bam file -o OUT_SAM, --out_sam OUT_SAM output sam file -f FASTQ, --fastq FASTQ fastq file used for mapping
Not recommended for large fastq files