Hi! I've been trying to use bedtools to annotate SNPs (get rsid for each SNP), however this seems to need a lot of memory and my jobs always get killed.
bedtools intersect -a ${file} -b ${dbsnp_file} -wa -wb > out.txt
Where dbsnp_file is the entire dbsnp database already sorted.
Any other tools? BioMart and VEP cannot handle the amount of variants I need them to (>100k variants)
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_quantum_girl_ •
1 answer
this seems to need a lot of memory
sort both files and use bedtools intersect -sorted
f you are trying to intersect very large files and are having trouble with excessive memory usage, please presort your data by chromosome and then by start position (e.g., sort -k1,1 -k2,2n in.bed > in.sorted.bed for BED files) and then use the -sorted option. This invokes a memory-efficient algorithm designed for large files.
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