how to get the nucleotide squence behind a symbolic ALT in VCF
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20 months ago
Maxine ▴ 50

I got a VCF that consists of structural variations via sniffles2. I find the contents in the ALT column sometimes are symbolic SVs, such as <INS> and , instead of nucleotide sequences. The VCF is like this:

#CHROM      POS   ID    REF   ALT   QUAL  FILTER      INFO  FORMAT      cy201704    cy201804    cy201904    cy202304
NC_058089.1 79333062    Sniffles2.INS.DF23M9    T     <INS> 37    PASS  PRECISE;SVTYPE=INS;SVLEN=7772;END=79333062;SUPPORT=8;COVERAGE=24,25,26,28,37;STRAND=+;AC=2;STDEV_LEN=0;STDEV_POS=0;SUPP_VEC=001000000000  GT:GQ:DR:DV:ID    0/0:0:22:0:NULL   0/0:0:31:0:NULL   1/1:60:0:40:Sniffles2.INS.13174S9   0/0:0:21:0:NULL

However, the nucleotide sequences are what I need for downstream analysis. Did anybody meet a similar problem before?

SV vcf sniffles • 410 views
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