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vcf2fasta on single sequence fasta - insert N for deletions #21

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GuitCos opened this issue Nov 30, 2023 · 0 comments
Open

vcf2fasta on single sequence fasta - insert N for deletions #21

GuitCos opened this issue Nov 30, 2023 · 0 comments

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@GuitCos
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GuitCos commented Nov 30, 2023

Hello,
I was wondering how the vcf2fasta tool deals with deletions of the type :
Contig284 3255757 . TGCC T 80.01 . AC=1;AF=1.00;AN=1;DP=2;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=34.00;QD=31.35;SOR=0.693 GT:AD:DP:GQ:PL 1:0,2:2:90:90,0

Is it possible to instruct vcf2fasta.py to replace the missing nucleotides with 'N's, as it seems it does not do it by default. Or maybe I have missed something ?

Thank you,

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