Number of reads supporting a structural variant value in Dragen structural variant calling output

Question

[ieie]

Hi,

I am writing because I would like to know if in the VCF output of Manta withing Dragen, if there is a way or a field value to see the number of reads supporting a structural variant, Output example from Manta user guide

chr1    11830208        MantaINS:1577:0:0:0:3:0 T       <INS>   999     PASS    END=11830208;SVTYPE=INS;CIPOS=0,12;CIEND=0,12;HOMLEN=12;HOMSEQ=TAAATTTTTCTT;LEFT_SVINSSEQ=TAAATTTTTCTTTTTTCTTTTTTTTTTAAATTTATTTTTTTATTGATAATTCTTGGGTGTTTCTCACAGAGGGGGATTTGGCAGGGTCACGGGACAACAGTGGAGGGAAGGTCAGCAGACAAACAAGTGAACAAAGGTCTCTGGTTTTCCCAGGCAGAGGACCCTGCGGCCTTCCGCAGTGTTCGTGTCCCTGATTACCTGAGATTAGGGATTTGTGATGACTCCCAACGAGCATGCTGCCTTCAAGCATCTGTTCAACAAAGCACATCTTGCACTGCCCTTAATTCATTTAACCCCGAGTGGACACAGCACATGTTTCAAAGAG;RIGHT_SVINSSEQ=GGGGCAGAGGCGCTCCCCACATCTCAGATGATGGGCGGCCAGGCAGAGACGCTCCTCACTTCCTAGATGTGATGGCGGCTGGGAAGAGGCGCTCCTCACTTCCTAGATGGGACGGCGGCCGGGCGGAGACGCTCCTCACTTTCCAGACTGGGCAGCCAGGCAGAGGGGCTCCTCACATCCCAGACGATGGGCGGCCAGGCAGAGACACTCCCCACTTCCCAGACGGGGTGGCGGCCGGGCAGAGGCTGCAATCTCGGCACTTTGGGAGGCCAAGGCAGGCGGCTGCTCCTTGCCCTCGGGCCCCGCGGGGCCCGTCCGCTCCTCCAGCCGCTGCCTCC  GT:FT:GQ:PL:PR:SR       0/1:PASS:999:999,0,999:22,24:22,32      0/1:PASS:999:999,0,999:18,25:24,20    0/0:PASS:230:0,180,999:39,0:34,0

chr1    17124941        MantaBND:1445:0:1:1:3:0:0       T       [chr1:234919886[T       999     PASS    SVTYPE=BND;MATEID=MantaBND:1445:0:1:1:3:0:1;CIPOS=0,1;HOMLEN=1;HOMSEQ=T;INV5;EVENT=MantaBND:1445:0:1:0:0:0:0;JUNCTION_QUAL=254;BND_DEPTH=107;MATE_BND_DEPTH=100 GT:FT:GQ:PL:PR:SR       0/1:PASS:999:999,0,999:65,8:15,51

I doubt it is either the PR or the SR fields. VCF fields description is there a way to infer it? Thanks

[Pierre Lindenbaum]

may be you want something like duphold ? https://github.com/brentp/duphold

Answer 1

[benformatics]

Check the MANTA manual:

https://github.com/Illumina/manta/blob/master/docs/userGuide/README.md

The last column chunk with 0/1 and PASS is likely the GT and FILTER so the colon separated values are as follows:

GT  Genotype
FT  Sample filter, 'PASS' indicates that all filters have passed for this sample
GQ  Genotype Quality
PL  Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification
PR  Number of spanning read pairs which strongly (Q30) support the REF or ALT alleles
SR  Number of split-reads which strongly (Q30) support the REF or ALT alleles

So the last two are PR and SR and I’m guessing the comma separates the REF and the ALT.

[ieie]

Thanks a lot for the answer! yes, I already saw those two fields, however I was wondering if there is a way to know the total number of reads supporting the structural variant, alternative in this case. I am doubting it is the sum of the PR and SR. What do you think?

[benformatics]

Yeah it would probably be the sum.