Holiday Notice:
The Frontline Support team will be slow to respond December 17-18 due to an institute-wide retreat and offline December 22- January 1, while the institute is closed. Thank you for your patience during these next few weeks. Happy Holidays!

How to interpret MuTect2 vcf file .?

AlvaAlva GermanyMember
edited February 2016 in MuTect v1

Hello All,

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 ?
and
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..

Thank you

Post edited by Alva on

Best Answer

Answers

Sign In or Register to comment.