can i merge many vcfs or I should do in realignment?

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6.7 years ago

Siavash Salek Ardestani ▴ 20

Hi I have 50 whole genome sequence data for SNP discovery. somebody say to me you should use all samples together for realignment and if I do realignment Separately for each sample then my results of SNP discovery will be wrong. I want to know is it true?

SNP realignment whole genome sequence • 1.3k views

ADD COMMENT • link updated 6.7 years ago by Biostar 20 • written 6.7 years ago by Siavash Salek Ardestani ▴ 20

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Do you have each sample in a separate VCF file? I ask because your post title mentions merging VCF files and your actual post has nothing on that.

ADD REPLY • link 6.7 years ago by Ram 44k

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yes. I would appreciate you guide me.

ADD REPLY • link 6.7 years ago by Siavash Salek Ardestani ▴ 20

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in realignment step I could realignment all samples together, then I had one bam file for SNP discovery .on the other hand I could realignment each sample separately. I want to know the result of these methods for SNP discovery is different?

ADD REPLY • link 6.7 years ago by Siavash Salek Ardestani ▴ 20

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I don't really know what that means, but AFAIK samples get realigned independently, giving you one BAM per sample. I am not sure if this information helps you.

ADD REPLY • link 6.7 years ago by Ram 44k

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