FILTER 'MQ' is not defined in the header

[kubranarci]

Have you checked the docs?

• nf-core website: troubleshooting
• nf-core modules documentation

Description of the bug

Main branch, annotation using annovar. Reported by @Naga

Command used and terminal output

Process:
NF_PLATYPUSINDELCALLING:PLATYPUSINDELCALLING:OUTPUT_STANDARD_VCF:BCFTOOLS_SORT
Error:
  [W::vcf_parse_filter] FILTER 'MQ' is not defined in the header
  Error encountered while parsing the input at chr1:10048
  Cleaning
Issue:
##FILTER=<ID=ALTC,Description="Alternative reads in control">
##FILTER=<ID=ALTT,Description="Less than three variant reads in tumor">
##FILTER=<ID=GTQ,Description="Quality for genotypes below thresholds">
##FILTER=<ID=GTQFRT,Description="Quality for genotypes below thresholds and variant allele frequency in tumor < 10%">
##FILTER=<ID=HapScore,Description="Too many haplotypes are supported by the data in this region.">
##FILTER=<ID=PASS,Description="Position passed all filters, call is made">
##FILTER=<ID=Q20,Description="Variant quality is below 20.">
##FILTER=<ID=QD,Description="Variant-quality/read-depth for this variant">
##FILTER=<ID=QUAL,Description="Quality of entry too low and/or low coverage in region">
##FILTER=<ID=VAF,Description="Variant allele frequency in tumor < ' + str(args.newpun) + ' times allele frequency in control">
##FILTER=<ID=VAFC,Description="Variant allele frequency in tumor < 5% or variant allele frequency in control > 5%">
##FILTER=<ID=alleleBias,Description="Variant frequency is lower than expected for het.">
##FILTER=<ID=badReads,Description="Variant supported only by reads with low quality bases close to variant position, and not present on both strands.">
##FILTER=<ID=strandBias,Description="Variant fails strand-bias filter">
MQ not in header..

Relevant files

No response

System information

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