Bam file metrics

Question

[Sabeen]

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

[GenoMax]

Qualimap (LINK) would be one good option for overall metrics. You will not get all the metrics you are looking from one package.

Answer 1

[heskett]

Samtools stats is a new option for this. samtools is very reliable and easy to use in my experience

[Ram]

Is it (samtools stat) fast though? I recall samtools being really slow compared to sambamba.

[heskett]

I don't know if its the fastest out there, but its certainly the most well adopted, well documented, and well supported. Any time you might save on computation would be offset by dealing with bugs or unreliable software from other groups

[Ram]

samtools is a high bar on widespread software use. sambamba is pretty reliable though. You may not use a random github repository tool, but published, benchmarked tools are fine, especially if they've been compared to samtools in performance metrics.