Record of commands run in header is incorrect

[kjwinfield]

This part:

echo '##bedtools_command=bedtools intersect' "$vcf_name" "$panel_bed_name" >> header.txt
bcftools view -h "${vcf_path}" | tail -n 1 >> header.txt

# Intersect with panel, normalise and reheader
bedtools intersect -header -u -a "$vcf_path" -b "$panel_bed_path" \
	| bcftools reheader -h header.txt -o "${vcf_prefix}_filtered.vcf"

https://github.com/eastgenomics/eggd_vep/blob/96615fef84b75ed2fa0618e18612cf5519b6599b/src/code.sh#L227C1-L232C69

writes to the header that the command run was bedtools intersect {sample_vcf} {panel_bed} when it is actually bedtools intersect -header -u -a {sample_vcf} -b {panel_bed}