Sort BAM by coordinate not name?

[tseemann]

The -bam output of MapCaller seems to be sorted by name. (like samtools sort -n)

Normally we want them sorted by coordinate (like samtools sort), so we can run samtools index and provide to other tools that assume coordinate sorting.

Could MapCaller produce coordinate-sorted BAMs ? Or does that not work because you align reads in order and write out results immediately?

To get around this I do this:

CPUS=18
MapCaller -i ref.fa -f R1.fq -f2 R2.fq -t $CPUS -no_vcf -bam - | samtools sort -@ $CPUS > out.bam

[hsinnan75]

@tseemann Yes, MapCaller aligns reads in order and writes out results immediately. Therefore, it takes another step to sort all read alignments.

[tseemann]

Ok - will keep using samtools sort. Thank you!