tried calculating CLR on Bovine50kSNP genotype data

[spchavan10]

Hello, I'm a masters scholar in animal genetics, I tried using sweed for calculation of CLR for detection of selection signatures, but when i saw the output file i.e. report file , its not giving the likelihood value to the positions mentioned in my vcf file
there are 26889 snps in my vcf file and the output file showed me the results of chromosome 1 only with 26889 likelihood values for random BPs which are not even in my vcf file

[alachins]

sweed calculates scores based on the grid size you set, not for the bp positions in your file. based on the grid size you choose and the bp positions in your file, sweed defines a linear grid of equidistant positions and evaluates them. It is unlikely that these positions will be the same as snp positions in your dataset.

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On Thu, Aug 29, 2024 at 6:51 AM Shambhuraditya Chavan < ***@***.***> wrote: Hello, I'm a masters scholar in animal genetics, I tried using sweed for calculation of CLR for detection of selection signatures, but when i saw the output file i.e. report file , its not giving the likelihood value to the positions mentioned in my vcf file there are 26889 snps in my vcf file and the output file showed me the results of chromosome 1 only with 26889 likelihood values for random BPs which are not even in my vcf file — Reply to this email directly, view it on GitHub <#30>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AALKWCXVRVGTIDQWVRR4RRDZT2SF3AVCNFSM6AAAAABNJS4N42VHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ4TGNBUG4ZDKOI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- Nikolaos Alachiotis

[spchavan10]

so what should I do to get the values for the desired positions? kindly reply as early as possible...

[spchavan10]

Or is it not recommended to use CLR on SNP chip genotype data? from what i understood from the manual, WGS data is highly recommended for SweeD