Some "FILTER" lines not defined in raw VCF header

[simondrue]

Hi,

I get the following error when trying to parse a raw (--qc-output-all) VCF from Sniffles2 (v2.4.0) through BCFtools:

[W::vcf_parse_filter] FILTER 'COV_CHANGE_DUP' is not defined in the header
[W::vcf_parse_filter] FILTER 'COV_CHANGE_DEL' is not defined in the header

I can see that COV_CHANGE_INS (and multiple others) are in the header, but these two seems to be missing.

For now I have implmented the following temporary fix by reheadering the VCFs manually:

# Fix header in raw VCF
# Get header and remove last line
bcftools view -h ${{TEMP_DIR}}/raw.vcf | head -n -1 > ${{TEMP_DIR}}/hdr.txt

# Add FILTER lines to header
echo '##FILTER=<ID=COV_CHANGE_DUP,Description="Coverage change filter for DUP">' >> ${{TEMP_DIR}}/hdr.txt
echo '##FILTER=<ID=COV_CHANGE_DEL,Description="Coverage change filter for DEL">' >> ${{TEMP_DIR}}/hdr.txt

# Add last line of header
bcftools view -h ${{TEMP_DIR}}/raw.vcf | tail -n 1 >> ${{TEMP_DIR}}/hdr.txt

# Reheader
bcftools reheader \
    --threads {cores} \
    --header ${{TEMP_DIR}}/hdr.txt \
    --output ${{TEMP_DIR}}/reheadered.vcf \
    ${{TEMP_DIR}}/raw.vcf

Hoping you can fix this soon

Thank you for a nice tool!

Kind regards,
Simon