Dear all,
I'm working on NGS data (HiSeq Illumina). After filtering the quality on my fastq data files . I have mapped my reads against a reference genome using bwa. I then generated a sam alignment file (sam then bam) and a vcf (containing the coordinates of my snps & indels) file using respectively bwa,samtools & bcftools.
I would like to know if there is any software capable of giving the coordinates of the regions where the reads are not mapping the reference? (consensus sequences)
Or do you have any idea how to get them?
Thank you .
I'm working on NGS data (HiSeq Illumina). After filtering the quality on my fastq data files . I have mapped my reads against a reference genome using bwa. I then generated a sam alignment file (sam then bam) and a vcf (containing the coordinates of my snps & indels) file using respectively bwa,samtools & bcftools.
I would like to know if there is any software capable of giving the coordinates of the regions where the reads are not mapping the reference? (consensus sequences)
Or do you have any idea how to get them?
Thank you .
Comment