Question: How to extract genomic positions of SNPs using snp-sites?
1
gravatar for pltbiotech_tkarthi
19 months ago by
CIMMYT, Mexico
pltbiotech_tkarthi180 wrote:

By using snp-sites (https://github.com/sanger-pathogens/snp-sites) I extracted the SNPs with Linux command: snp-sites file name.fasta. This script just extracting the SNPs without position information. I know the genomic positions of my reference sequence. My question is: How to add the genomic position of reference sequence to the aligned fasta sequences as an input to obtain the result of SNPs with genomic positions information as an output. Please let me know an additional script to extract genomic positions of SNPs output from the aligned fasta sequences, besides the SNPs extracting script (snp-sites file name.fasta). Related post: C: How to extract SNPs from multiple alignment fasta file?.

sequencing snp alignment genome • 860 views
ADD COMMENTlink modified 4 weeks ago by Jorge Amigo12k • written 19 months ago by pltbiotech_tkarthi180
0
gravatar for christine
4 weeks ago by
christine0
christine0 wrote:

Hey, wonder if you find a solution? I'm also looking for this..

ADD COMMENTlink written 4 weeks ago by christine0
0
gravatar for Jorge Amigo
4 weeks ago by
Jorge Amigo12k
Santiago de Compostela, Spain
Jorge Amigo12k wrote:

There's an optional vcf output format:

https://github.com/sanger-pathogens/snp-sites#output

You should be able to get the positions from that resulting vcf file.

ADD COMMENTlink written 4 weeks ago by Jorge Amigo12k
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