Whole Genome Sequencing (WGS) Alignment Quality check softwares/tools

Question

[ravi.uhdnis]

Hi,

I use BWA to align my WGS human data reads from illumina HiSeq2500 machine against GRCh38 as reference genome. Although BWA provide certain basic information about the mapping done (e.g. % of mapped reads etc) but Is there any software/tools which can provide me such information in greater details, kind of overall alignment quality matrix ?.

[Ashutosh Pandey]

Will this help: https://broadinstitute.github.io/picard/picard-metric-definitions.html#CollectWgsMetrics.WgsMetrics

Answer 1

[Brian Bushnell]

BBMap supports extensive quality-related output histograms. For example:

bbmap.sh ref=hg19.fa in1=read1.fq in2=read2.fq mhist=mhist.txt ihist=ihist.txt ehist=ehist.txt qhist=qhist.txt qahist=qahist.txt indelhist=indelhist.txt

...and various others. That will generate the files mhist.txt, which shows the rates of match, substitution, insertion, deletion, and N at each base position; ihist, the insert size histogram; and so forth (they're documented in the shell script). They're all tab-delimited columns, so they're easy to plot in R or Excel.

Answer 2

[ravi.uhdnis]

Thank you Guys. I found "Qualimap" is a good software for knowing the quality of Alignment run. The reference article is here.