My aim is looking for SNP and allele count differences between samples. I will use samtools mpileup to get a VCF file.
First, I used BOWTIE for alignment.
For single end fastq files
bowtie -S -q -p 8 -a --best -V2 -m 1 --strata Referans file.txt
How can I do it for paired end reads ? file1.txt and file2.txt
For Snp calling, I allowed 2 mismatches. Do you suggest any different command for alignment?
Thanks for any help.