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1,440 bytes added
, 21:44, 25 February 2016
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| REF ATTTG | | REF ATTTG |
| ALT GTTTC #CLUMPED, 1 ts, 1 tv | | ALT GTTTC #CLUMPED, 1 ts, 1 tv |
− | ALT ATTTC #SNP, 1 tv | + | ALT ATTTC #SNP, 1 tv, note that we get the SNP after truncating the bases ATTT to reveal a G/C transversion SNP |
| #since all the alleles are of the sample length, classified as MNP too. | | #since all the alleles are of the sample length, classified as MNP too. |
| | | |
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| ALT <CN4> #SV | | ALT <CN4> #SV |
| ALT <CN12> #SV | | ALT <CN12> #SV |
| + | |
| + | =Interesting Variant Types = |
| + | |
| + | Adjacent Tandem Repeats from lobSTR's tandem repeat finder panel. <br> |
| + | |
| + | |
| + | 20 9538655 <span style="color:#FF0000">ATTTATTTATTTATTTATTTATTTATTTATTTATTTATT</span><span style="color:#0000FF">CATTCATTCATTCATTCATTCATTC </span> <STR> |
| + | |
| + | This can be induced as |
| + | |
| + | one record considering only the ATTT repeats |
| + | 20 9538655 <span style="color:#FF0000">ATTTATTTATTT </span> <span style="color:#FF0000">ATTT </span> |
| + | |
| + | one record with CATT repeats |
| + | 20 9538695 <span style="color:#0000FF">CATTCATT </span> <span style="color:#0000FF">CATT </span> |
| + | |
| + | one record with a mix of both repeat types |
| + | 20 9538695 <span style="color:#FF0000">TATT<span style="color:#0000FF">CATTCATT </span> <span style="color:#0000FF">CATT </span> |
| + | |
| + | = Representation of close by variants = |
| + | |
| + | 1:124001690 |
| + | TTTCTTT--CAAAAAAAGATAAAAAGGTATTTCATGG |
| + | TTTCTTTAAAAAAAAAAGATAAAAAGGAATTTCATGG |
| + | |
| + | a single complex variant |
| + | CHROM POS REF ALT |
| + | 1 124001690 C AAA |
| + | |
| + | an Indel and SNP adjacent to one another |
| + | CHROM POS REF ALT |
| + | 1 124001689 T TAA |
| + | 1 124001690 C A |
| + | |
| + | Representing it as a single complex variant enforces that both "indel" and "SNP" are always together. |
| + | Representing it as 2 separate variants allows both alleles to segregate independently. |
| | | |
| = Output = | | = Output = |