Comments (8)
I'm getting the same error while trying to extract SNPs from MAFFT alignments of coronavirus, courtesy of GISAID
(pangenomics) ubuntu@ip-172-31-29-49:~/covid19/vcf$ snp-sites -v -o GISAID0201 ../gisaid_hcov-19_2021_01_30_08.fasta.gz
Alignment ../gisaid_hcov-19_2021_01_30_08.fasta.gz contains sequences of unequal length. Expected length is 29766 but got 29768 in sequence hCoV-19/Japan/PG-9988/2020|EPI_ISL_902711|2020-07
Also, wasn't there an option to output a VCF per sample?
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@rderelle @dbrami got any solution for this? any other tool or something?
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@Logan1x
I have abandoned Mauve, which doesn't seem to work well.
It is actually easy to get a list of SNPs from Minimap2 (using third party pgm provided in the same package) or GSalign (directly from the pgm).
cheers
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fxxk!
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Hi,
I'm wondering if folks might recommend a similar tool to extract SNPs from a multiple sequence alignment to generate an alignment of SNPs only? I am similarly running into errors with Expected length although I have confirmed that sequences are the same length.
Thank you in advance!
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Hi,
Did anybody find solution?
Thanks
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