record.FILTER vs. record.FILTERS

[jaime11]

Hello:

I am using this library to read a VCF file that has been filtered (GATK Mutect2 + FilterMutectCalls) such as:

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT LH00280_109_22KKWNLT3_3_GAGTTACC LH00280_109_22KKWNLT3_3_GTGCTATG
chr1 610724 . T C . germline;map_qual;weak_evidence AS_FilterStatus=weak_evidence,map_qual;AS_SB_TABLE=3,2|1,1;DP=7;ECNT=1;GERMQ=1;MBQ=20,20;MFRL=204,173;MMQ=52,27;MPOS=18;NALOD=0.477;NLOD=0.601;POPAF=2.13;ROQ=14;TLOD=4.17 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:4,0:0.250:4:1,0:0,0:2,0:2,2,0,0 0/1:1,2:0.500:3:1,1:0,0:1,1:1,0,1,1
chr1 27006684 . C T . PASS AS_FilterStatus=SITE;AS_SB_TABLE=114,107|3,2;DP=233;ECNT=1;GERMQ=93;MBQ=20,20;MFRL=209,166;MMQ=60,60;MPOS=25;NALOD=1.91;NLOD=24.03;POPAF=6.00;ROQ=22;TLOD=7.14 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:105,0:0.012:105:36,0:36,0:80,0:58,47,0,0 0/1:116,5:0.047:121:44,1:33,2:80,3:56,60,3,2

In the FILTER column, the file can contain either a list of filters, such as in the first variant (bold) or PASS as in the second.

When I iterate the variants:

vcf = VCF(vcf_file, threads = THREADS)
writer = Writer(output_vcf, vcf)

for record in vcf:

In variants where I have a list of filters, FILTER just contains the ";" separated string and FILTERS contains the list of elements corresponding to that list, however when there is "PASS" in the filter, record.FILTER is None but record.FILTERS is ["PASS"]

Shouldn't the second case have the string "PASS" in record.FILTER?

Thank you.

[brentp]

hi, there are other issues on this. It's basically a design mistake that I made when starting out and now am hesitant to change for backward compatibility. If record.FILTER is "PASS", then cyvcf2 thinks there's no FILTER and so returns None.