I have used samtools mpileup, and bcftools call/filter (v1.5) to call SNPs between 2 samples and a de novo reference transcriptome.
Here is my pipeline:
bcftools mpileup -Ou -f ref.fa aln.bam1 aln.bam2 | \ bcftools call -Ou -mv | \ bcftools filter -s LowQual -e '%QUAL<20 || DP>100' > var.flt.vcf
I'm interested in extracting SNPs that occur between individual samples (aln.bam1 and aln.bam2) , and not between the samples and the reference (aln.bam 1 and ref.fa, aln.bam2 and ref.fa) . I would like to see how different each sample is different, or similar, from one another. Is this possible? I haven't been able to find much documentation on how one would approach this.
Any info would be greatly appreciated.