Is uniq working as expected?

[watronfire]

In the new addition to the variant calling script, you concatenate the BED files from BCFtools filtering and the depth mask. I noticed you used the uniq command, which I assume you're using to remove redundant positions in the resulting BED file.

illumina-vc/scripts/call_variants.sh

Lines 181 to 182 in fb2c31e

	cat $DIR/03_variants/$SAMPLENAME.vcffiltered.bed $DIR/04_assembly/$SAMPLENAME.depthmask.bed | \
	uniq > $DIR/04_assembly/$SAMPLENAME.allmask.bed

However, uniq only filters adjacent matching lines, so the stream needs to be sorted beforehand. You should be able to prepend a sort command before uniq to remove redundant lines. Not terribly critical, but might reduce the size of the resulting file and prevent some issues from and out of spec BED file.