Different sorting in bam and bed

[gubrins]

Heys,

I am having problems when trying to calculate coverage levels of a bed file with genomeCoverageBed (v2.3), as my bam and bed files are sorted differently:

cut -f 1 combined_after_scaffolding.bed |uniq scaffold_1 scaffold_10

samtools view -H both_not_filtered_sorted.bam àHD VN:1.6 SO:queryname àSQ SN:scaffold_1 LN:233710445 àSQ SN:scaffold_2 LN:214025719

However, when I try to sort it with the genome.file like this: bedtools sort -g genomefile.txt -i combined_after_scaffolding.bed > sorted.bed

My computer rans out of memory (250Gb). Any solutions to that?

Thanks in advance!