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Hello!
This line https://github.com/ucscCancer/fpfilter-tool/blob/master/fpfilter.pl#L498 seems to cause problems, according to https://github.com/vcftools/vcftools/blob/master/src/perl/Vcf.pm#L3028
vcf-annotate FAILES on fpfiltered VCF-file:
Error 1:
Leading or trailing space in attr_key-attr_value pairs is discouraged:
[ InputVCFSource] [fpfilter]
Error 2:
Can't use string ("--vcf-file /outputs/77013075gdc."...) as a HASH ref while "strict refs" in use at /soft/vcftools-0.1.16/share/perl/5.26.1/Vcf.pm line 2950, <__ANONIO__> line 196.
Specification (https://docs.gdc.cancer.gov/Encyclopedia/pages/TCGA_VCF_1.1v2/) doesn't help to fix this line...
For now I had to simply change the line:
# push @$parsed_header, qq{##vcfProcessLog=<InputVCF=<$input>, InputVCFSource=<fpfilter>, InputVCFVer=<6.0>, InputVCFParam=<"$param_string"> InputVCFgeneAnno=<.>>\n}, $column_header;
push @$parsed_header, qq{##fpfilterCommand="$param_string"\n}, $column_header;
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