Question: merging VCF files or not
0
gravatar for Sara
29 days ago by
Sara50
Sara50 wrote:

I am working with VCF file (one file per sample) and the goal is to report the genes with mutation. so, my question is since I have many files and at the end I need to have one file as report, shall I merge the files or I need to do something else?

snp vcf • 189 views
ADD COMMENTlink modified 28 days ago • written 29 days ago by Sara50
2

Sure, why wouldn't you?

ADD REPLYlink written 29 days ago by WouterDeCoster41k

If the boss asks for one file, you give one file =)

ADD REPLYlink written 28 days ago by gb1.0k

Also, no real advantage to keeping things separate, I guess.

ADD REPLYlink written 28 days ago by WouterDeCoster41k

@ WouterDeCoster: Ok Thanks. then I will merge the files using bcftools and then parse the new file. is that correct?

ADD REPLYlink written 28 days ago by Sara50

Please respond to guillaume.rbt's question. Note, that, if you merge all VCFs together, you can still produce a separate annotation file for each sample using ANNOVAR.

ADD REPLYlink modified 28 days ago • written 28 days ago by Kevin Blighe50k

What do you mean by "report the genes with mutation", can you give more details?

ADD REPLYlink written 29 days ago by guillaume.rbt660

@guillaume.rbt: to make it clear let me rephrase my question. I have many VCF files and I want to summarize all of them into a csv file. the csv file should have some columns including gene names, REF and ALT per sample(file). so, now the question is: how should I organize all the data from all samples in one csv file? do you have any experience?

ADD REPLYlink written 28 days ago by Sara50

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized. SUBMIT ANSWER is for new answers to original question.

ADD REPLYlink written 28 days ago by genomax73k
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