Entering edit mode
5.2 years ago
Sara
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260
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?
Sure, why wouldn't you?
If the boss asks for one file, you give one file =)
Also, no real advantage to keeping things separate, I guess.
@ WouterDeCoster: Ok Thanks. then I will merge the files using bcftools and then parse the new file. is that correct?
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.
What do you mean by "report the genes with mutation", can you give more details?
@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?
Please use
ADD COMMENT/ADD REPLYwhen responding to existing posts to keep threads logically organized.SUBMIT ANSWERis for new answers to original question.yes you can do it, by using git bash to merge all vcf/HapMap files in one file. cat *hmp.txt >all_comine.txt
That would not be a valid VCF file and definitely not useful in any way.