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Revision as of 21:44, 25 February 2016
, 21:44, 25 February 2016→Representation of close by variants
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.
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 =
