I would like to call SNP's and indels from my data which has 30 samples of which 20 samples are of one genotype and other 10 are from other genotype. I have a reference sequence which is a 1 mb qtl sequence. Which is the best way to call SNP's? I tried Mosaik but its aligning approximately 50% of reads and also bwa-sw which aligns ~90-95% of my reads. so i thought of using samtools / mpileup and bcftools as told at this link and this link
But my concern is how to differentiate with my genotypes? changing read names accordingly and where can i specify to consider 20 as one group and 10 as another group to classify SNPs? Suggestions please..
But my concern is how to differentiate with my genotypes? changing read names accordingly and where can i specify to consider 20 as one group and 10 as another group to classify SNPs? Suggestions please..
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