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How to interpret MuTect2 vcf file .?
I have VCF file from MuTect2 after running the following command line... Or is there any where explained the vcf file from MuTect2 ? I hve used the recommend [[https://broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_cancer_m2_MuTect2.php](https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_cancer_m2_MuTect2.php] method for finding the variants.
Here is log file after running MuTect2,
INFO 04:04:13,507 VectorLoglessPairHMM - Time spent in setup for JNI call : 92.38734281100001
INFO 04:04:13,509 PairHMM - Total compute time in PairHMM computeLikelihoods() : 168922.088975422
INFO 04:04:13,511 MuTect2 - Ran local assembly on 31353 active regions
INFO 04:04:13,694 ProgressMeter - done 3.137161264E9 59.8 h 68.0 s 100.0% 59.8 h 0.0 s
INFO 04:04:13,697 ProgressMeter - Total runtime 215445.99 secs, 3590.77 min, 59.85 hours
INFO 04:04:13,699 MicroScheduler - 15135399 reads were filtered out during the traversal out of approximately 145467009 total reads (10.40%)
INFO 04:04:13,701 MicroScheduler - -> 6960 reads (0.00% of total) failing BadCigarFilter
INFO 04:04:13,703 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
INFO 04:04:13,704 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
INFO 04:04:13,705 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
INFO 04:04:13,707 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
INFO 04:04:13,708 MicroScheduler - -> 15128439 reads (10.40% of total) failing NotPrimaryAlignmentFilter
INFO 04:04:13,709 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
And the output VCF file looks like this..For one variant,
chr1 14522 . G A . alt_allele_in_normal;t_lod_fstar ECNT=1;HCNT=4;MAX_ED=.;MIN_ED=.;NLOD=30.30;TLOD=4.04 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/0:169,5:0.026:4:1:0.800:5740,170:108:61
In which As I have the normal and tumor samples I am looking for Number pof ref and variants alleles from both Normal and Tumor samples...
But I cannot find those in the above file. Could you please walk me a little bit here..
1. why for all variants it has only alt_allele_in_normal ?
2. And where is the alternate allele information from the Tumor sample ?
3. what does this mean GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 ?
I saw the information in the header for the above part but I didn't understand it correctly..