If any read contains N (streaches of N), BWA usually replace it with any of four nucleotides randomly.
My confusion is whether these replaced nucleotides are taken under consideration while calling variants. Looking for your comments.
Paul I Costea
Popular answer
bwa will replace N's in the reference with a random nucleotide. However, N's in the read remain N's.
SAMTools will use the original reference so the bwa indexing scheme won't matter. Thus, this little bwa trick will in no way influence your variant calling.
5 votes
3 thanks
Paul I Costea
bwa will replace N's in the reference with a random nucleotide. However, N's in the read remain N's.
SAMTools will use the original reference so the bwa indexing scheme won't matter. Thus, this little bwa trick will in no way influence your variant calling.
5 votes
4 thanks
- Badges
- Science topic
- Similar topics
- Bioinformatics
- Bioinformatics and Computational Biology
More Sourav Nayak's questions See All
Similar questions and discussions