samtools-bam-processing

To sort and index BAM files for NGS analysis, use command-line tools to sort by coordinate or read name and generate index files, enabling efficient random access required for downstream variant calling.

Converting CRAM files to BAM may require a reference FASTA for CRAM operations, as CRAM encoding relies on the reference sequence, though some basic conversions might proceed depending on the specific data embedded.

Generating quality control statistics for alignment files involves using command-line utilities to calculate mapping rates, insert sizes, and coverage depth, providing essential metrics to evaluate NGS pipeline performance.

Filtering sequencing reads by mapping quality in BAM files uses command-line flags to extract reads meeting specific quality thresholds or FLAG bit criteria, removing low-confidence alignments before downstream analysis.

Processing SAM, BAM, and CRAM files with this toolkit requires samtools 1.17 or higher to ensure compatibility with the latest format specifications and command-line features for alignment file manipulation.

Marking or removing PCR duplicates from BAM files involves using command-line tools to identify and flag or eliminate redundant reads, ensuring accurate quantification and reducing bias in downstream variant calling.