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campanam / vcf2aln

Script to convert multi-sample VCFs to FASTA alignments
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Alignment of ancient and modern data #11

Open ModiShrushti opened 1 month ago

ModiShrushti commented 1 month ago

Hi Michael, Thanks for such a useful script. I am trying to convert a vcf file that has both modern and ancient samples and the script is working fine when I am using parameters (-q 30 -y 5 -x 90 -s) but it is not concatenating the individual sample files if I am removing -s (-x 90 -q 30 -c). Also, I am unsure if the parameters I use are suitable for modern and ancient data. Could you please suggest a set of parameters ideal for low coverage and ancient data?

Thanks Shrushti

campanam commented 1 month ago

Hello Shrushti,

I am unable to diagnose the issues without knowing more about your project and input files. Is there an email I can contact you?

Thanks,

Michael

ModiShrushti commented 1 month ago

Hi Michael, Thanks for the quick response. My email is @.***

Best Shrushti

Shrushti Modi, Ph.D., Post-Doctoral Research Fellow Laboratories of Molecular Anthropology and Microbiome Research (LMAMR) University of Oklahoma Norman Email Address: @., @.

On Thu, Aug 15, 2024 at 2:04 PM Michael G. Campana @.***> wrote:

Hello Shrushti,

I am unable to diagnose the issues without knowing more about your project and input files. Is there an email I can contact you?

Thanks,

Michael

— Reply to this email directly, view it on GitHub https://github.com/campanam/vcf2aln/issues/11#issuecomment-2292008428, or unsubscribe https://github.com/notifications/unsubscribe-auth/AUFH5JWGQPJVA3WSCIA2FSDZRT3TFAVCNFSM6AAAAABMQU2RNGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEOJSGAYDQNBSHA . You are receiving this because you authored the thread.Message ID: @.***>