What Change In Samfile

Question

[Sara]

Hi everyone,

I have a Sam files and I applied different other analysis but i don't know which column add or change when we applied these steps.

example: I aligned the sequence with BWA 1- realigned with GATK 2- markduplicate PICARD

I don't know which column change on original samfiles when we applied these steps?

Could you please help?

Thanks

Sara

Answer 1

[Wen.Huang]

1- realign: the CIGAR string changes, the start position of alignment may also change, these only affecte those that are realigned by GATK 2- markduplicate: the bitwise flag change, depending on whether you ask picard tools to remove the duplicated reads