Question: merging VCF files or not
0
gravatar for Sara
6 months ago by
Sara90
Sara90 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 • 314 views
ADD COMMENTlink modified 4 months ago by zubairzube0 • written 6 months ago by Sara90
2

Sure, why wouldn't you?

ADD REPLYlink written 6 months ago by WouterDeCoster43k

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

ADD REPLYlink written 6 months ago by gb1.7k

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

ADD REPLYlink written 6 months ago by WouterDeCoster43k

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

ADD REPLYlink written 6 months ago by Sara90

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 6 months ago • written 6 months ago by Kevin Blighe56k

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

ADD REPLYlink written 6 months ago by guillaume.rbt770

@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 6 months ago by Sara90

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 6 months ago by genomax80k

yes you can do it, by using git bash to merge all vcf/HapMap files in one file. cat *hmp.txt >all_comine.txt

ADD REPLYlink written 4 months ago by zubairzube0
2

That would not be a valid VCF file and definitely not useful in any way.

ADD REPLYlink written 4 months ago by WouterDeCoster43k
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