What Change In Samfile
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12.2 years ago
Sara ▴ 170

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

samtools • 1.8k views
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1
Entering edit mode
12.2 years ago
Wen.Huang ★ 1.2k

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

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