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Query regarding getCpgPositions.pl script input file #1

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devenderarora opened this issue Nov 12, 2020 · 0 comments
Open

Query regarding getCpgPositions.pl script input file #1

devenderarora opened this issue Nov 12, 2020 · 0 comments

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@devenderarora
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devenderarora commented Nov 12, 2020 •
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Respected Sir,
I read you paper and found this very interesting. Sir, I have a query regarding variant call file (.vcf) as an input. Is this file is the output from WGS data? and do this vcf file need phasing before processing.
I tried calling:

getCpgPositions.pl genome.fa snp.vcf allele
But it ended up with use of uninitialized value at $number
May I know if I am doing correctly.

Any lead will be of great help.
Thanking You
Regards
Devender Arora
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@devenderarora