why Mutect2 calls some germline variants as somatic ones?
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7 months ago
cocchi.e89 ▴ 190

I am using Mutect2 to call somatic variants on some human hg38 whole genome sequencing data. I noticed that some variants are called (and PASS all filters) both as somatic and germline in the same sample. As example:

Germline:

chr19   39826873    .   A   C   975.79  PASS    ANN=C|missense_variant|MODERATE|DYRK1B|ENSG00000105204|Transcript|ENST00000323039|protein_coding|9/11||ENST00000323039.9:c.1210T>G|ENSP00000312789.4:p.Phe404Val|1490|1210|404|F/V|Ttc/Gtc|||-1||SNV|HGNC|HGNC:3092||deleterious(0.01)||chr19:g.39826873A>C,C|splice_region_variant&intron_variant|LOW|DYRK1B|ENSG00000105204|Transcript|ENST00000348817|protein_coding||9/11|ENST00000348817.7:c.1132-6T>G|||||||||-1||SNV|HGNC|HGNC:3092||||chr19:g.39826873A>C,C|splice_region_variant&intron_variant|LOW|DYRK1B|ENSG00000105204|Transcript|ENST00000430012|protein_coding||8/10|ENST00000430012.6:c.1096-6T>G|||||||||-1||SNV|HGNC|HGNC:3092||||chr19:g.39826873A>C,C|missense_variant|MODERATE|DYRK1B|ENSG00000105204|Transcript|ENST00000593685|protein_coding|9/11||ENST00000593685.5:c.1210T>G|ENSP00000469863.1:p.Phe404Val|1679|1210|404|F/V|Ttc/Gtc|||-1||SNV|HGNC|HGNC:3092|YES|deleterious(0.01)||chr19:g.39826873A>C,C|splice_region_variant&intron_variant|LOW|DYRK1B|ENSG00000105204|Transcript|ENST00000597639|protein_coding||8/10|ENST00000597639.5:c.1132-6T>G|||||||||-1||SNV|HGNC|HGNC:3092||||chr19:g.39826873A>C,C|downstream_gene_variant|MODIFIER|DYRK1B|ENSG00000105204|Transcript|ENST00000600611|protein_coding|||||||||||3009|-1|cds_end_NF|SNV|HGNC|HGNC:3092||||chr19:g.39826873A>C,C|downstream_gene_variant|MODIFIER|DYRK1B|ENSG00000105204|Transcript|ENST00000601696|retained_intron|||||||||||1529|-1||SNV|HGNC|HGNC:3092||||chr19:g.39826873A>C,C|downstream_gene_variant|MODIFIER|DYRK1B|ENSG00000105204|Transcript|ENST00000601972|protein_coding|||||||||||3333|-1||SNV|HGNC|HGNC:3092||||chr19:g.39826873A>C,C|downstream_gene_variant|MODIFIER|MIR6719|ENSG00000277759|Transcript|ENST00000622428|miRNA|||||||||||2843|-1||SNV|HGNC|HGNC:50012|YES|||chr19:g.39826873A>C;BaseQRankSum=-2.735;CSQ=C|missense_variant|MODERATE|DYRK1B|ENSG00000105204|Transcript|ENST00000593685|protein_coding|9/11||ENST00000593685.5:c.1210T>G|ENSP00000469863.1:p.Phe404Val|1679|1210|404|F/V|Ttc/Gtc|||-1||SNV|HGNC|HGNC:3092|YES|||5|P1|CCDS12543.1|ENSP00000469863|Q9Y463.196|A0A024R0I0.58|UPI0000001059|Q9Y463-1||1|deleterious(0.01)|probably_damaging(0.998)|Gene3D:1.10.510.10&Pfam:PF00069&PROSITE_profiles:PS50011&PANTHER:PTHR24058&PANTHER:PTHR24058:SF12&SMART:SM00220&Superfamily:SSF56112&CDD:cd14226|||||||||||||||||||||||||||||||||32|4.502689|||||||||||||32|||||||||||||||||||T&T|-0.09&-0.09|4.49||||U|0.000000|L&L|1.855&1.855|D&D&D|0.99999&1&1|D&D|1.0&1.0|D&D|0.999&0.999|0.86047|0.632|||||||||||DYRK1B&DYRK1B|||||||||||||||||||||||||||||;ExcessHet=3.5655;FS=0;InbreedingCoeff=-0.1304;MQ=60;MQRankSum=0;QD=11.76;ReadPosRankSum=-0.661;SOR=0.647;VQSLOD=21.37;culprit=MQRankSum;DP=372;AF=0.115;MLEAC=3;MLEAF=0.115;PG=0,6,17;AN=2;AC=1  GT:AD:DP:FT:GQ:PL:PP    0/1:15,18:33:HET:99:408,0,390:402,0,401 ./.:.:.:.:.:.:.

Somatic:

chr19   39826873    .   A   C   .   PASS    AS_SB_TABLE=8,9|8,12;ECNT=1;GERMQ=13;GENE=ENSG00000105204.14;DP=73;AS_FilterStatus=SITE;MBQ=37,37;MFRL=221,292;MMQ=60,60;MPOS=41;POPAF=7.3;TLOD=54.32;CSQ=C|missense_variant|MODERATE|DYRK1B|ENSG00000105204|Transcript|ENST00000593685|protein_coding|9/11||ENST00000593685.5:c.1210T>G|ENSP00000469863.1:p.Phe404Val|1679|1210|404|F/V|Ttc/Gtc|||-1||SNV|HGNC|HGNC:3092|YES|||5|P1|CCDS12543.1|ENSP00000469863|Q9Y463.196|A0A024R0I0.58|UPI0000001059|Q9Y463-1||1|deleterious(0.01)|probably_damaging(0.998)|Gene3D:1.10.510.10&Pfam:PF00069&PROSITE_profiles:PS50011&PANTHER:PTHR24058&PANTHER:PTHR24058:SF12&SMART:SM00220&Superfamily:SSF56112&CDD:cd14226|||||||||||||||||||||||||||||||||32|4.502689|||||||||||||32|||||||||||||||||||T&T|-0.09&-0.09|4.49||||U|0.000000|L&L|1.855&1.855|D&D&D|0.99999&1&1|D&D|1.0&1.0|D&D|0.999&0.999|0.86047|0.632|||||||||||DYRK1B&DYRK1B|||||||||||||||||||||||||||||    GT:AD:AF:DP:F1R2:F2R1:SB    ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. 0/1:17,20:0.541:37:9,13:8,7:8,9,8,12    ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. 0/1:16,18:0.516:34:11,11:5,7:5,11,6,12  ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. ./.:.:.:.:.:.:.

Why is that happening and how is it possible?

somatic germline haplotypecaller mutect2 • 246 views
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Please post also the whole Mutect2 command used

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