to mark the duplicates

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4.5 years ago

manubiomed20 ▴ 10

I did a complete genome assembly and generated archivi bam. Now I need to mark the duplicates and I could not. How do I solve this problem?

Assembly • 1.0k views

ADD COMMENT • link updated 8 months ago by Ram 41k • written 4.5 years ago by manubiomed20 ▴ 10

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You should really provide some more information for people to be able to help you.

ADD REPLY • link 4.5 years ago by Asaf 10k

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Well, what did you try?

ADD REPLY • link 4.5 years ago by swbarnes2 13k

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gatk MarkDuplicates \INPUT=home/ims.santos06/bam/SRR062634.bam\ 
                     OUTPUT=home/ims.santos06/bam/SRR062634_markduplicates.bam

ADD REPLY • link updated 4.5 years ago by Ram 41k • written 4.5 years ago by manubiomed20 ▴ 10

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ADD REPLY • link 4.5 years ago by swbarnes2 13k

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Were there any error messages?

ADD REPLY • link 4.5 years ago by Kevin Blighe 86k

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I used this command:

gatk MarkDuplicates \INPUT=home/ims.santos06/bam/SRR062634.bam\ 
                     OUTPUT=home/ims.santos06/bam/SRR062634_markduplicates.bam

ADD REPLY • link updated 4.5 years ago by Ram 41k • written 4.5 years ago by manubiomed20 ▴ 10

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Please do not add answers unless you're answering the top level question. The content you added belongs in the top level post, so please edit the post and add the content there.
Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

ADD REPLY • link 4.5 years ago by Ram 41k

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