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Bidimensional SFS #9

Open adria-boada opened 3 days ago

adria-boada commented 3 days ago

Good evening,

ngsPool provides poolSFS.R, a script which estimates a one dimensional SFS from the SAF.GZ output file. Is it possible for other software to read pairs of "sample allele frequency log-likelihoods" from ngsJulia and estimate a bidimensional SFS?

I do know about an implementation in ANGSD: "Fast and accurate estimation of multidimensional site frequency spectra from low-coverage high-throughput sequencing data". Would it be possible to translate the SAF files from ngsJulia so that they can be read by ANGSD? I have been unable to accomplish so.

ANGSD documentation

Requirements, at the end of the article cited above:

The program is implemented in a fast multi-threaded C++ program and takes as input either BAM/CRAM files or BCF/VCF files containing genotype likelihood files as produced from standard tools such as GATK or SAMtools.

Kind regards, Adrià.

mfumagalli commented 2 days ago

Good point. Can you please contact me separately via email to continue this conversation (and about the other points you raised) separately?

From: adria-boada @.> Sent: 10 November 2024 7:33 PM To: mfumagalli/ngsJulia @.> Cc: Subscribed @.***> Subject: [mfumagalli/ngsJulia] Bidimensional SFS (Issue #9)

Good evening,

ngsPool provides poolSFS.R, a script which estimates a one dimensional SFS from the SAF.GZ output file. Could you please recommend other software to read pairs of "sample allele frequency log-likelihoods" and estimate a bidimensional SFS?

I do know about an implementation in ANGSD: "Fast and accurate estimation of multidimensional site frequency spectra from low-coverage high-throughput sequencing data"https://doi.org/10.1093/gigascience/giac032. Would it be possible to translate the SAF files from ngsJulia so that they can be read by ANGSD? I have been unable to accomplish so.

Kind regards, Adrià.

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