Forum:Variant calling (SNV/InDel): is only using properly paired reads recommended?

Question

[Ian]

Hello,

For a while now my variant calling workflow (SNVs and InDels) has filtered mapped reads from BWA to remove discordantly mapped reads, i.e. keeping only properly paired reads, and remove secondary alignments.

samtools view -f2 -F256

Obviously for identifying structural variants this would hamper the analysis. For identifying SNVs and Indels is what I am doing good or bad?

Thank you.