Representing tandem repeats in VCF

[dennishendriksen]

Dear @readmanchiu,

The Variant Call Format Specification v4.4. and v4.5 were released recently. One of the major changes is support for (short) tandem repeats, see section 5.7 which contains the following example:

##fileformat=VCFv4.5
##INFO=<ID=SVLEN,Number=A,Type=Integer,Description="Length of structural variant">
##INFO=<ID=CN,Number=A,Type=Float,Description="Copy number of allele">
##INFO=<ID=RN,Number=A,Type=Integer,Description="Total number of repeat sequences in this allele">
##INFO=<ID=RUS,Number=.,Type=String,Description="Repeat unit sequence of the corresponding repeat sequence">
##INFO=<ID=RUL,Number=.,Type=Integer,Description="Repeat unit length of the corresponding repeat sequence">
##INFO=<ID=RUC,Number=.,Type=Float,Description="Repeat unit count of corresponding repeat sequence">
##INFO=<ID=RB,Number=.,Type=Integer,Description="Total number of bases in the corresponding repeat sequence">
##INFO=<ID=CIRUC,Number=.,Type=Float,Description="Confidence interval around RUC">
##INFO=<ID=CIRB,Number=.,Type=Integer,Description="Confidence interval around RB">
##INFO=<ID=RUB,Number=.,Type=Integer,Description="Number of bases in each individual repeat unit">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phase set">
##FORMAT=<ID=CN,Number=1,Type=Float,Description="Copy number">
##ALT=<ID=CNV:TR,Description="Tandem repeat determined based on DNA abundance">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample
chr1 100 cnv_notation T <CNV:TR>,<CNV:TR> . . SVLEN=30,30;CN=3,0.9666;RUS=CAG,CAG,CA,CAG;RN=1,3;RB=90,15,2,12 GT:PS:CN 1|2:100:3.9666
chr1 117 precise_alt2 AG A . . GT:PS 0|1:100
chr1 130 precise_alt1 G GCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG . . GT:PS 1|0:100

For downstream tools it would be helpful if Straglr outputs STRs according to this new specs. What are your thoughts?

Best regards,
@dennishendriksen

[readmanchiu]

Most definitely, thanks for the suggestion!

[readmanchiu]

VCF v4.5 (CNV:TR representation) has been implemented in the latest release (v1.5.2)