Mutect2 output vcf file is not giving any QUAL scores

Hi team GATK,
Greetings from India!

I am running GATK4 for somatic variant calling

gatk Mutect2 -R ../../11_reference_genome/ref_gen_chr1_22_X_Y_final.fa --tumor-sample 01T -I 01T_sorted.bam -I 01N_sorted.bam -O out_01_Mutect2.vcf

I am new to GATK and Variant analysis, kindly help me in this:
The output file is showing results as:
1. VCF output from MUTECT2:

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 01N 01T

chrY 353035 . A G . . DP=2;ECNT=1;POP_AF=5.000e-08;TLOD=8.14 GT:AD:AF:DP:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB ./. 0/1:0,2:1.00:2:0,2:0,0:0,39:0,858:40:3:0.99
chrY 353881 . T G . . DP=2;ECNT=1;POP_AF=5.000e-08;TLOD=7.98 GT:AD:AF:DP:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB ./. 0/1:0,2:1.00:2:0,2:0,0:0,38:0,858:40:12:0.9
chrY 2648923 . G A . . DP=10;ECNT=2;POP_AF=5.000e-08;TLOD=24.79 GT:AD:AF:DP:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB ./. 0/1:0,6:0.857:6:0,3:0,3:0,38:0,763:

Q1 : Why QUAL column is giving output as "." for all the calls. None of the variants in 3GB file have quality score.
Q2 : How to predict this file as 01N is giving "./." , is it like keeping 01N as base "0/1:0,2:1.00:2:0,2:0,0:0,39:0,858:40:3:0.99" (chrY first call) are the changes/variations happening in 01T sample?

After running Mutect2, I run FilterMutectCalls function:

gatk FilterMutectCalls -V out_01_Mutect2.vcf -O out_01_Mutect2_filtered.vcf

Output is:

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 019N 019T

chrY 353035 . A G . read_position DP=2;ECNT=1;POP_AF=5.000e-08;P_CONTAM=0.00;P_GERMLINE=NaN;TLOD=8.14 GT:AD:AF:DP:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB ./. 0/1
chrY 353881 . T G . PASS DP=2;ECNT=1;POP_AF=5.000e-08;P_CONTAM=0.00;P_GERMLINE=NaN;TLOD=7.98 GT:AD:AF:DP:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB ./. 0/1:0,2:1.0
chrY 2648923 . G A . PASS DP=10;ECNT=2;POP_AF=5.000e-08;P_CONTAM=0.00;P_GERMLINE=-2.406e+00;TLOD=24.79 GT:AD:AF:DP:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB ./. 0/1
chrY 2648954 . G A . PASS DP=6;ECNT=2;POP_AF=5.000e-08;P_CONTAM=0.00;P_GERMLINE=-1.541e+00;TLOD=11.39 GT:AD:AF:DP:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB ./. 0/1
chrY 2649246 . C A . PASS DP=2;ECNT=1;POP_AF=5.000e-08;P_CONTAM=0.00;P_GERMLINE=NaN;TLOD=7.98 GT:AD:AF:DP:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB ./. 0/1:0,2:1.0

It adds "Pass", "str_contraction;t_lod", "bad_haplotype;clustered_events" etc to the Filter column, my question here are:

Q3: There is no QUAL value, how can we say that the variant is PASS or not?
Q4: How to filter potential somatic variant from this huge vcf file, what are the things one should keep in mind while filtering for somatic variants?

I know, there are n-number of research papers online about this, I am just curious about your ideas and many people like me, who are new to the domain, they can get answers under one umbrella.

Till now what I have understood is:
Depth >=30, Filter = PASS, Quality >=30
should be the parameters one should apply to filter variants. Snpshift and snpeff are used for annotations and filtering results, kindly correct me if I am wrong!!
Any help will be highly appreciated!

Thanks
Ajay Katoch

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