Hello all,

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.

Regards, sabeen