Question: (Closed) Merge selective vcf files into one vcf file using a single command
0
gravatar for jaybee
13 months ago by
jaybee40
South Korea
jaybee40 wrote:

Hello

I have a directory named "set" where I have 4 sets namely set1, set2, set3, and set4. Each set has 50 Indel vcf files and 50 SNP vcf files. The files are vcf.gz format along with their index files, .vcf.gz.tbi.

In each set, for Indel as well as for SNP, I created a list for only the vcf files (before creating their respective index files) using

for i in *.vcf.gz;
do ls > vcfindel1.list
done

[vcfindel1.list is the list of vcf files of the indels in set 1 ONLY]

It creates a list file for every indel and SNP for each set.

Now, I use merge command to merge all 50 vcf files into One vcf file using:

command="bcftools merge -Ob -m none " ;

while read vcfindel1
do
    command="${command}"" ""${vcfindel1}" ;
done < vcfindel1.list

command="${command}"" -o ProjectMerge.bcf" ;

echo `$command` ;

bcftools index ProjectMerge.bcf ;

But, I receive the error message:

vcfindel1.list unknown file type

Anybody can help me solve this?

bcftools wes merge vcf • 690 views
ADD COMMENTlink modified 13 months ago by Pierre Lindenbaum127k • written 13 months ago by jaybee40

Hello jaybee!

We believe that this post does not fit the main topic of this site.

I closed this post as I have received the solution of my question.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 13 months ago by jaybee40
3
gravatar for Pierre Lindenbaum
13 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum127k wrote:

don't

for i in *.vcf.gz;
do ls > vcfindel1.list
done

but

ls *.vcf.gz > vcfindel1.list

or

find . -type f -name "*.vcf.gz" > vcfindel1.list

Then use simply something like:

bctools merge -m none --file-list   vcfindel1.list -O z -o out.vcf.gz
ADD COMMENTlink modified 13 months ago • written 13 months ago by Pierre Lindenbaum127k

Woah! It works !! Thank you! :)

ADD REPLYlink written 13 months ago by jaybee40
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