Calculate Aligment Metrics For Ngs Data (Zero Mismatches And Uniquely Mappable Reads)

Question

[User6891]

Hi,

I want to calculate some aligment quality metrics from whole exome data (paired-end Illumina).

I used the picard tool CollectAlignmentSummaryMetrics which provides me already with some scores. However I also want to know the percentage of reads with zero mismatches and the percentage of uniquely mappable reads, which seems not possible with the picard tool. The data were aligned with BWA.

Does anyone know a tool to calculate both metrics?

Answer 1

[Ashutosh Pandey]

I dont know any tool but you can use tags in the BAM file to answer these questions.

XM tag gives you number of mismatches in the alignment w.r.t reference genome. So write a small code that will parse this information. XM:i:1 means there was one mismatch.

XT tag will give you if the read was uniquely matched or not. For example, XT:A:U tag will be present in bam file for every read that is uniquely aligned.