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
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!!! :)