How To Split Multiple Samples In Vcf File Generated By Gatk?

Question: How To Split Multiple Samples In Vcf File Generated By Gatk?

5.6 years ago by

United States

newDNASeqer • 630 wrote:

I did variant calling using BWA + PiCard + GATK and have just got the filtered VCF files from GATK. In the process of running GATK, I used list of inputs (11 samples) and for most steps, I had only one output file for each step. Now, I got two VCF files (one for SNPs and the other is for indels), each of which contains 11 samples. I can see the names of the 11 samples in the header of vcf files, and each sample seems to have one column of data. So I am wondering how to split each VCF files into individual sample vcf files?

From my search, vcf tools seems to have the capability of splitting vcf, but I could not find an example for splitting multiple samples. Can someone please help me? Thanks a lot

vcf gatk split • 18k views

ADD COMMENT • link •

modified 23 months ago by Biostar ♦♦ 20 • written 5.6 years ago by newDNASeqer • 630

SelectVariants

ADD REPLY • link written 2.7 years ago by Medhat ♦ 8.2k

4.4 years ago by

Jorge Amigo ♦ 11k

Santiago de Compostela, Spain

Jorge Amigo ♦ 11k wrote:

I know this is an old question but, as I've already stated in this post, there's a very efficient way of doing this that hasn't been reported yet. hope it helps:

for file in *.vcf*; do
  for sample in `bcftools view -h $file | grep "^#CHROM" | cut -f10-`; do
    bcftools view -c1 -Oz -s $sample -o ${file/.vcf*/.$sample.vcf.gz} $file
  done
done

EDIT: bcftools query -l lists all samples, so the fastest loop would be the following:

for file in *.vcf*; do
  for sample in `bcftools query -l $file`; do
    bcftools view -c1 -Oz -s $sample -o ${file/.vcf*/.$sample.vcf.gz} $file
  done
done

ADD COMMENT • link modified 21 months ago • written 4.4 years ago by Jorge Amigo ♦ 11k

This one is at least 10 times faster than the vcf-subset

ADD REPLY • link written 3.7 years ago by wqshi.nudt • 20

This one is great... You seriously made my day todAY. THANKS A LOT.

ADD REPLY • link written 2.7 years ago by ste.arnoux • 0

You're the man! Best solution ever!

ADD REPLY • link written 18 months ago by she.xinwei • 0

It works perfectly. Could you explain how does the latest part of the third line, '-o ${file/.vcf/.$sample.vcf.gz} $file', works? I know it has nothing to do with the BCF and it is just basic bash renaming but I cant figure out how can I google it (I mean what to actually write in the search bar), and I found it quite useful for any script (so I got cleaner, clearer file names). I understand how it works in this case but I'll like to learn a bit more.

Thank you

ADD REPLY • link modified 17 months ago • written 17 months ago by Carles Borreda • 0

sure. since you will be generating a file per sample you could just simply use -o $sample.vcf.gz, but I personally prefer to keep the original file name to know where that data came from. for that reason I use .o ${file/.vcf*/.$sample.vcf.gz}, which uses a bash string manipulation function to substitute anything from .vcf to the right of the original file name for .$sample.vcf.gz. the result is a single file name for each sample that keeps the original file name (but the .vcf or .vcf.gz extension) before the sample name.

ADD REPLY • link written 17 months ago by Jorge Amigo ♦ 11k

bash string manipulation

This is what I was looking for. Yeah I understand what you are doing but I didn't know it was possible, I was just using ${file}.${sample}.vcf.gz, but I ended up with a foo.vcf.bar.vcf.gz.sample.vcf, which is quite annoying. I didn't know that it was possible to change $file on the fly. Not that I know I'll add this to may of my scripts. Thank you!

ADD REPLY • link written 17 months ago by Carles Borreda • 0

5.6 years ago by

Neilfws ♦ 48k

Sydney, Australia

Neilfws ♦ 48k wrote:

You want vcf-subset, with the -c option:

-c, --columns <string>           File or comma-separated list of columns to keep in the vcf file. If file, one column per row

So if your sample is named S1 and you want a VCF file for only that sample named S1.vcf:

vcf-subset -c S1 bigfile.vcf > S1.vcf

There are examples on the VCFtools documentation page, but they are unhelpfully labelled "Stripping columns".

ADD COMMENT • link written 5.6 years ago by Neilfws ♦ 48k

Is the bcftools view faster than vcf-subset for subsetting since it uses the new htslib?

ADD REPLY • link modified 4.4 years ago • written 4.4 years ago by smilefreak • 400

it should be. in fact, on the vcftools page you can read the following note: "A fast HTSlib C version of this tool is now available (see bcftools view)."

ADD REPLY • link written 4.4 years ago by Jorge Amigo ♦ 11k

5.6 years ago by

William • 4.4k

Europe

William • 4.4k wrote:

Use GATK SelectVariants -sn mySampleName to extract a single sample from a multiple sample vcf.

http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantutils_SelectVariants.html

You can specify multiple sample names to keep, but if you want to extract all 11 to a separate vcf file you need to run the command 11 times.

I would try try to stick to the GATK vcf prostprocessing tools, because you also generated the vcf with GATK, and there is always the chance another tool set has a different interpretation of the same format. (And I don't trust tools written in Perl, but that is just my personal bias. )

ADD COMMENT • link written 5.6 years ago by William • 4.4k

It is a good idea to use the same toolkit as much as possible to avoid things getting "lost in translation" between tools. Some tools out there do not enforce format specifications strictly enough and you can end up with files that are not compatible with other tools.

ADD REPLY • link written 5.3 years ago by vdauwera • 890

Thank you! I was not aware of GATK selectvariants can do it and was writing my own code.

Here are the updated links to the post: http://gatkforums.broadinstitute.org/gatk/discussion/54/selecting-variants-of-interest-from-a-callset https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_variantutils_SelectVariants.php

ADD REPLY • link written 22 months ago by DVA • 500

5.6 years ago by

Ashutosh Pandey ♦ 11k

Philadelphia

Ashutosh Pandey ♦ 11k wrote:

vcf-subset is what you need. But you may find this post from another forum helpful.

http://seqanswers.com/forums/showthread.php?t=24711

ADD COMMENT • link written 5.6 years ago by Ashutosh Pandey ♦ 11k

5.6 years ago by

alexej.knaus • 120

Berlin

alexej.knaus • 120 wrote:

go to www.Gene-Talk.de , upload your vcf file with multiple patients, let it preproocess and download single files, or analyze singe or multiple vcf files.

ADD COMMENT • link written 5.6 years ago by alexej.knaus • 120

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