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I couldn't make it work with bedtools, because my genome's index file is corrupted, but this should work for others:

I couldn't make it work with bedtools, because my genome's index file is corrupted, but this should work for others who have successfully used bwa or samtools to index their reference genome:

I couldn't make it work with bedtools, because my genome's index file is corrupted, but this should work for others:

blat -stepSize=5 -repMatch=2253 -minScore=20 -minIdentity=0 -out=pslx /genomes/mm10.fa.qz query.fa output.pslx
awk 'NR>5 {print $14 "\t" $16-10"\t" $17+10}' output.pslx > regions.bed
bedtools getfasta -fi /genomes/mm10.fa.gz -bed regions.bed

blat -stepSize=5 -repMatch=2253 -minScore=20 -minIdentity=0 -out=pslx /genomes/mm10.2bit query.fa output.pslx

blat -stepSize=5 -repMatch=2253 -minScore=20 -minIdentity=0 -out=pslx /genomes/mm10.fa.qz query.fa output.pslx