Hi,
My goal is to conduct variant calling and phase variants using samtools v 1.0 and HAPCUT.
I was wondering what is the appropriate way to deal with PCR/optical duplicates if the goal is variant calling in a heterozygous sample? I was using Picard Suite's MarkDuplicates and removing duplicates, but does this identify duplicates as those read pairs with identical external coordinates? Because this would then preclude calling heterozygous variants, correct? Is there a better approach for removing only reads which have identical external coordinates AND have exactly the same sequence?
Thank you!
My goal is to conduct variant calling and phase variants using samtools v 1.0 and HAPCUT.
I was wondering what is the appropriate way to deal with PCR/optical duplicates if the goal is variant calling in a heterozygous sample? I was using Picard Suite's MarkDuplicates and removing duplicates, but does this identify duplicates as those read pairs with identical external coordinates? Because this would then preclude calling heterozygous variants, correct? Is there a better approach for removing only reads which have identical external coordinates AND have exactly the same sequence?
Thank you!