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how do you find the sequence of a long insertion? #441
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As an update, I have tried --genotype-vcf and it did not print out the genotype ie: sniffles |
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I get this output in my vcf file
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE
Ad-ED119.9_ECJ9+CMV-JnJ-StabWuS-SV40-dsRNA 18587 Sniffles2.INS.3S0 N 56 PASS PRECISE;SVTYPE=INS;SVLEN=8050;END=18587;SUPPORT=1609;COVERAGE=87914,88129,88187,88034,87662;STRAND=+;NM=0.032;AF=0.099;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=1608 GT:GQ:DR:DV ./.:60:79428:8759
so the insertion is at position 18587, but I can't figure out what the sequence is. Is there a way to print that out?
Thanks
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