Entering edit mode
6.3 years ago
Tania
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180
Hi every one
If we have this variant:
GT:GQ:DP:VF:GQX:PL:AD ==> 0/1:99:910:0.095:99:549,0,17114:824,86
And it did not pass, it is reported as LowVariantFreq
I understand that this is because AD =824,86. which means we have 824 reads support the ref and 86 only support the alt.
But it is a stop gain variant, so I wanna double check before throwing it. Is it artefact? Should be ignored or still of interest? Does it mean the patient is mosaic for example?
Thanks
Hi , What is your variant (del ins snv ) ? what is the context of this base ? low complexity region or not ? this 2 points should help you to decide the reality of your variant.
Best
I don't know about the region, how do we know? it is: G -> A AC=42;AF=0.5;AN=80;DP=27355;EXON;FC=Missense_V425I;GI=SUCLG2;QD=17.62;SF=2,3,9,13,16,17,19,24,26,27,28,30,33,43,44,49,75,86,89,91,93,96,100,101,102,104,105,113,114,117,123,124,127,129,131,132,133,134,135,137;TI=NM_001177599
and 0/1:99:910:0.095:99:549,0,17114:824,86
You can have look with the genomic position and the chromosome
Makes complete sense that the variant gets discarded since it has such a low frequency, but there are still 86 reads supporting the alternative allele there. Best you can do is validate with another sequencing technology.
Agreed WouterDeCoster , but for example with SANGER she got low chance to confirmed, it's the eternal question i think we have to wait more precise and low cost technologies like one cells target to my mind ...
Thanks WouterDeCoster and Titus so much.
Nobody asked if this is a tumour or germline sample? If tumour, then low frequency is expected; if germline, then variants should ideally be called at a 50:50 split between ref and alt reads. The frequency of this region is a bit worrying if it's a germline sample and you should look at the alignments in the BAM file over the region in which the variant is called - use IGV to view the alignments.
Valid question, but I consider information like that up to the OP to provide.
By the way mosaic problematic (low fraction) and tumour are quite close in bioinfomatique analysis...
Yes, but it was neither specifically stated if this sample was expected to show mosaicism or not. On the contrary, it was just posed as a question if the low frequency meant that mosaicism could be present. No-one's to know other than the OP, who should be well versed on the source of the sample and the history of the individual from which it was taken.
What mean OP (English is not my maternal language and to me acronym are not easy sorry) ? original post ? If i understand your the problem concerned details not enough in the original post is that you mean ?
Hi Titus! Yes, 'OP' means 'original poster', i.e., Tania. The problem is that there was not enough information in the question (a common problem on Biostars); so, the result of that is that we either speculate (guess) or ask for more information.
Thanks!
Hi Kevin, How can I know if it mosaicism or not? We have an individual with a very rare phenotype, what else we can check to decide? I don't have any more information about him, but could ask. But what information I should relate to this?
You haven't told us anything about the source of the sample. Blood? Transformed lymphocytes? Tissue biopt? Hereditary or acquired phenotype?