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faircloth-lab / phyluce

software for UCE (and general) phylogenomics
http://phyluce.readthedocs.org/
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SNP calling #253

Closed leonvarhan closed 2 years ago

leonvarhan commented 2 years ago

Hello, I was wondering what were the tools or programs in Phyluce 1.7.1 for SNP calling after phasing UCE data. Is phyluce_snp_screen_phased_alignments no longer supported ? Thank you for your time !!!

brantfaircloth commented 2 years ago

Hello. It is no longer supported. The SNPs calls in phased alignments should be in each of the *.0.vcf and *.1.vcf files. I've not continued to maintain additional formatting tools because there are a number of options out there (e.g. vcf2fasta, vcftools, plink, etc.). That said, phyluce_snp_screen_phased_alignments should run just fine if you install an older version of phyluce (in a conda environment, for instance).

leonvarhan commented 2 years ago

Thank you Dr. Faircloth. I did run phyluce_snp_screen_phased_alignments and it generated thousands of files, one random SNP per UCE locus. I haven't figured out yet how to merge them for further analysis, but I will try the phasing workflow in Phyluce 1.7.1 to get the .vcf files. I really appreciate your time and help!