Comments (4)
ONeillMB1
commented on July 20, 2024
1
Great tool! We also are very impressed with the speed!
Building off the recommendation of @tseemann, it would also be nice to be able to impose thresholds for tolerable amounts of missing data. For example, if 75% of samples in the alignment have data and there exists a SNP among them, retain the data in the SNP alignment.
from snp-sites.
andrewjpage
commented on July 20, 2024
1
I've added in a 'pure' mode as discussed with @tseemann and a 'keep monomorphic' mode (so it will work with BEAST).
from snp-sites.
jamiethompson77
commented on July 20, 2024
This does work with amino acids though right?
from snp-sites.
tseemann
commented on July 20, 2024
@jamiethompson77 i think AGTC is quite hard-coded into the tool, sorry. snp is in the name and that is DNA specific.
from snp-sites.
Related Issues (20)
- error: alignment contains sequences of unequal length HOT 8
- snp-sites docker install issue
- Improvement: let user specify pure and ambiguous bases
- snp-sites for all ~2 million SARS-COV-2 genomes in GISAID HOT 1
- What does *STAR* in ALT stand for HOT 3
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- How to understand `monomorphic sites`? HOT 1
- ./configure: line 3036: syntax error near unexpected token `CHECK,check' ./configure: line 3036: `PKG_CHECK_MODULES(CHECK,check >= 0.8.2,have_check="yes",'
- How to specify the reference sequence
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- How to know the interested SNP position in genome?
- Warning: No SNPs were detected so there is nothing to output HOT 1
- how to visualize VCF file in artemis?
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- 32 bit signed integer error HOT 1
- Warning: No SNPs were detected so there is nothing to output HOT 1
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- How to manage heterozygosity in SNP conversion?
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from snp-sites.