SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
GATK: sorting vcf file given a reference file jorge Bioinformatics 4 01-14-2015 12:16 PM
Problem with vcf file generated amruta.bn Bioinformatics 0 01-05-2012 03:22 AM
GATK: VCF file for Local realignment around indels jorge Bioinformatics 2 10-10-2011 11:15 PM
Converting Dindel VCF file to GATK BED file MolecularToast Bioinformatics 2 09-24-2011 06:38 PM
BAMseek large file viewer - now with VCF and FASTQ support BAMseek Bioinformatics 1 07-25-2011 06:57 PM

Reply
 
Thread Tools
Old 03-02-2012, 10:33 AM   #1
slowsmile
Member
 
Location: long island

Join Date: May 2011
Posts: 22
Default extremely large vcf file generated by GATK

Dear All
I am new to snp analysis and am recently working on GATK pipeline to identify snps on the whole genome data.

I went through the stage I raw data processing protocol recommended by GATK pipeline and generated an aligned, duplicate marked, and recalibrated BAM file for one of my samples.

I tried to run the Unified genotyper with the following code (for both snps and indels)

Quote:
java -Xmx4g -jar GenomeAnalysisTK.jar \
-l INFO \
-R /media/edrive/RNAseq/ucsc.hg19.fasta \
-T UnifiedGenotyper \
-I /media/edrive/RNAseq/LID46437/bwa/reads.recal.bam \
-o /media/edrive/RNAseq/LID46437/bwa/output.vcf \
--genotype_likelihoods_model BOTH \
--output_mode EMIT_ALL_CONFIDENT_SITES

exit
The code has been running for more than 20 hours yet has not completed. The in put bam file (reads.recal.bam) is only 11GB but as I checked the size of output vcf file, it already reached 60GB.

I just want to ask whether this is normal to take such a long time to run Unified genotyper and generates an excessively large vcf file?

Can anyone with experiences tell me: what is the size of your output vcf file when you work on the whole human genome? And how long does it take to run Unified genotyper usually?

Thanks a lot
slowsmile is offline   Reply With Quote
Old 03-02-2012, 10:45 AM   #2
shawpa
Member
 
Location: Pittsburgh

Join Date: Aug 2011
Posts: 72
Default

When I ran unified genotyper for the first time I was a bit confused by the "output" mode. You selected emit_all_confident_sites. Another researcher told me that he believed that choosing this as your output would output any site that is listed as variable in the population but not necessarily your sample. So you could get sites where your sample is homozygous for the reference rather than it outputing only the variants. I ran unified genotyper under default mode on a 80GB file and I think it only took like 8 hours at the most (over 24 processors).

I wouldn't take my word for it, but maybe someone else will post.
shawpa is offline   Reply With Quote
Old 12-09-2012, 08:23 PM   #3
kissthefuture
Junior Member
 
Location: china

Join Date: Apr 2011
Posts: 6
Default

Quote:
Originally Posted by slowsmile View Post
Dear All
I am new to snp analysis and am recently working on GATK pipeline to identify snps on the whole genome data.

I went through the stage I raw data processing protocol recommended by GATK pipeline and generated an aligned, duplicate marked, and recalibrated BAM file for one of my samples.

I tried to run the Unified genotyper with the following code (for both snps and indels)



The code has been running for more than 20 hours yet has not completed. The in put bam file (reads.recal.bam) is only 11GB but as I checked the size of output vcf file, it already reached 60GB.

I just want to ask whether this is normal to take such a long time to run Unified genotyper and generates an excessively large vcf file?

Can anyone with experiences tell me: what is the size of your output vcf file when you work on the whole human genome? And how long does it take to run Unified genotyper usually?

Thanks a lot

You may chose --output_mode EMIT_VARIANTS_ONLY instead.
kissthefuture is offline   Reply With Quote
Reply

Tags
gatk vcf size

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 04:53 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO