Question: can i merge many vcfs or I should do in realignment?
0
gravatar for siyavash_damdar
9 months ago by
siyavash_damdar20 wrote:

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?

ADD COMMENTlink modified 9 months ago by Biostar ♦♦ 20 • written 9 months ago by siyavash_damdar20

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 REPLYlink written 9 months ago by RamRS19k

yes. I would appreciate you guide me.

ADD REPLYlink written 9 months ago by siyavash_damdar20

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 REPLYlink written 9 months ago by siyavash_damdar20

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 REPLYlink modified 9 months ago • written 9 months ago by RamRS19k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1027 users visited in the last hour