hardfilter error

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18 months ago

bestone ▴ 30

I got the vcf file without Picard addgroup before making it. but I realized that it was wrong while making hard filter. I did some research and they told me to do a recall bam but I searched and couldn't find any information about it. Can you help me with this issue?

bam recall • 776 views

ADD COMMENT • link 18 months ago by bestone ▴ 30

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I think you are asking about how to add ReadGroups to an existing BAM. If that is true then you need this: https://gatk.broadinstitute.org/hc/en-us/articles/360037226472-AddOrReplaceReadGroups-Picard-

ADD REPLY • link 18 months ago by GenoMax 147k

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Thank you for your reply, Actually, I wanted to ask. After making Picard Markduplicates, I got a vcf file directly with gatk without making ReadGroups, so I made a mistake. People said that I could fix this error by doing a recall bam, but I couldn't find any information about it. how can I fix this error?

ADD REPLY • link 18 months ago by bestone ▴ 30

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because when I hardfilter the vcf file I saw that I made a mistake

ADD REPLY • link 18 months ago by bestone ▴ 30

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