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How to explain a variant present in PON is classified as PASS in the output using MuTect2
How to explain a variant present in PON is classified as PASS in the output (do not filtered as panel_of_nomal) using Mutect2.
The VCF corresponding to this variant in the PON file (called normal.vcf) is
15 9100143 . TG T . PASS AC=16;AF=0.500;AN=32;ECNT=1;MAX_ED=.;MIN_ED=.;NLOD=0.00;RPA=4,3;RU=G;STR;set=Intersection GT:AD:AF:ALT_F1R2:ALT_F2R1:QSS:REF_F1R2:REF_F2R1 0/1:0,65:1.00:34:31:0,2037:0:0 0/1:0,84:1.00:43:41:0,2754:0:0 0/1:0,66:1.00:28:38:0,2082:0:0 0/1:1,46:0.976:17:29:29,1394:0:1 0/1:0,78:1.00:28:50:0,2414:0:0 0/1:0,62:1.00:24:38:0,1862:0:0 0/1:0,74:1.00:29:45:0,2261:0:0 0/1:0,58:1.00:31:27:0,1789:0:0 0/1:0,73:1.00:23:50:0,2219:0:0 0/1:0,56:1.00:20:36:0,1680:0:0 0/1:0,51:1.00:21:30:0,1584:0:0 0/1:0,71:1.00:41:30:0,2197:0:0 0/1:0,66:1.00:37:29:0,2001:0:0 0/1:0,88:1.00:40:48:0,2635:0:0 0/1:0,61:1.00:23:38:0,1898:0:0 0/1:0,40:1.00:15:25:0,1195:0:0
MuTect2 is called as
java -Djava.io.tmpdir=_tmp/javaio -Xmx80G -jar GenomeAnalysisTK.jar -T MuTect2 -nct 20 \
-I:tumor _in/EU1.bam -PON _in/normal.vcf -o _out/EU1.vcf \
-R ../../../REFERENCES/GATKResourceBundle/GRCm38.fa \
-L ../../../REFERENCES/enrichment/Regions.interval_list --dbsnp ../../../REFERENCES/GATKResourceBundle/Mus_musculus.vcf.gz
And the output line is
15 9100143 . TG T . PASS ECNT=1;HCNT=1;MAX_ED=.;MIN_ED=.;NLOD=0.00;RPA=4,3;RU=G;STR;TLOD=182.36 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:0,60:1.00:29:31:.:0,1895:0:0
Tha same happened in other 14 tumor samples. All of then have called this variant as somatic instead of germline.
Note that the normal.vcf (PON) file was created not just calling normal tissues un --artifact_mode); therefore has genotype field of many samples. ¿Could be this the problem?.
Thank in advance