BWA mem bam output name sorted

Question

[User000]

Hello,

I have a sorted bam file (bwa mem alignment). Now I need to mark and remove duplicates using samtools. Before it asks me to do collate and fixmate then sort and then markdup. I was wondering if bam output (without sorting) is already name sorted (bwa version 0.7.17)? So I could skip unnecessary sorting, collating steps and after alignment pass directly to fixmate?

[Arup Ghosh]

BWA does not provide sorted bam file as output. If you want to check whether the aligned file is sorted or not use the following command.

samtools view -H <BAM file name> | grep SO

Answer 1

[ATpoint]

The alignment output (if without further manipulation) is grouped by name since fastq is grouped by name. Therefore you can pipe this directly into fixmate, e.g.:

bwa mem (...options) | samtools fixmate -m - - | samtools sort -o sorted.bam

The -m option of fixmate adds the mate tags which are required for the markdup command. The file must also be coordinate-sorted whereas fixmate requires files to be grouped or sorted by name.

samtools markdup sorted.bam markdup.bam