BWA and mapping

Question

[Juan Ledesma]

Hi everybody

I am Juan and I am very very new in this community. I am starting doing NGS data analysis and I have some doubts.

I using BWA to map my reads against a reference sequence. Afterwards I convert the sam file into a bam file that I can use to get a consensus sequence.My doubt is whether the sam/bam file I get after the mapping includes paired reads as well as the unpaired reads matching the reference sequence or only the paired reads and removes the reads as they don't have a mate.

Thanks in advance

Juan

[Juan Ledesma]

Thanks for your help

Answer 1

[Ashutosh Pandey]

It will have both reads for a pair irrespective of whether one of them remained unmapped or mapped at too many positions. The second column in the BAM file will be properly flagged as explained here: http://broadinstitute.github.io/picard/explain-flags.html