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What Change In Samfile

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
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updated by Wen.Huang Wen.Huang • written by Sara • Sara

1 answer

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

• 1 views • link
written by Wen.Huang Wen.Huang

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