I am new to NGS analysis and still learning things.
Currently i am trying to get bam files metrics. i used the gatk CollectAlignmentSummaryMetrics command. but i didnt get all information i need . preferably the following metrics.
Total reads in bam file total reads passing mapping quality filter total reads mapping to multiple genomic locations total reads in covered regions Median QV bases used in variant calling average read length total high quality mapped bases total reads +/- 100bp covered target regions total reads +/- 200bp covered target regions
please let me know if there is another way of bam file metrics.
Thanks in advance.
Qualimap(LINK) would be one good option for overall metrics. You will not get all the metrics you are looking from one package.