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Can´T Find The Snps With Samtools (Only Get Indels)

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Hello everybody,

Could anyone tell me how to get SNPs using SAMtools???. I am learning how to do it but can´t get the SNPs, I only get the Indels. I am working with a mutant I created from an E coli genome (just for practice). The mutant was created with 5 mismatches, 5 insertions and 5 deletions (using Biopieces).

The lenght and coverage is here:

read_fasta -i  <fasta ref genome>.fna | shred_seq -s 100 -c 50 | add_ident -k SEQ_NAME | write_fasta -x -o  <rrreads>.fna

The alignment was made with BWA . Then I used SAMtools protocol (as described in some of the posts) like this :

samtools mpileup -uf <refgenome>.fasta result.sort.bam > results.bcf

and then ,

bcftools view -vcg results.bcf - > test.vcf

If anyone can help me .. Thanks!!! :)


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