Dan Bolser
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What to use to determine SNPs in a population? How to find significant SNP variation between generations?
1 votes

First focus on calling SNPs accurately. See the BWA, SAMtools, BCFtools pipeline (as described here) or GATK4 (as described here). Once you have the [BV]CFs, then just code up the analysis to see ...

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Convert SNP data from GEO into PED and MAP files?
1 votes

Sadly the 'contact us' email at GEO didn't help at all. I ended up probably re-inventing the wheel with this script: https://gist.github.com/CholoTook/60968e3ab6d90cb8fd19be55a25592f1 YMMV

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Perl convert GFF3 file
0 votes

Your file looks like it is CDS feature based, not exon feature based, which seems to be what the script expects. There is a tool to convert CDS based GFF to exon based that I've used successfully in ...

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Use biopython to align SeqRecords stored in dict
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This BioPython document should get you started. A specific example is given here.

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Getting translation table of organisms through Entrez direct (or other CLIs)
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You can find them here at least: https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi You can download the complete list of codes (using FTP) here. However, to link a specific organism to a ...

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Obtaining HGDP project data in fasta format
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You can download HGDP data in FASTQ format here: https://www.internationalgenome.org/data-portal/data-collection/hgdp

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