This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Does it make sense to repeat the assembly step in variant calling?

Since the mapping step is non-deterministic, would it make sense to generate another BAM file with the same FASTQ file and same config with the objective of analyzing if a new variant is detected?

Thank you very much

variant calling
• 1,018 views • link
updated by Biostar Biostar • written by ajuiwl • ajuiwl

1 answer

No, since the results are at the very least "mostly deterministic" (I assume you're using bowtie2, which is the only aligner I know of that mentions this). It's vastly more efficient to simply filter with a reasonable MAPQ threshold.

• 1 views • link
written by Devon Ryan Devon Ryan

Thank you for your answer!!

• 1 views • link
written by ajuiwl • ajuiwl

Log in to answer this question.

More posts like this