Here to bother you again :-)
I currently use GATK a lot to analyze sequencing data, but many steps took really long time.
In the wiki on GATK parallelism, they recommend to use scatter/gather to speed up. However, I dont fully understand how to do it.
First, how to merge the results of scatter/gather ? For example, codes from GATK wiki:
gsa1> java -jar GenomeAnalysisTK -R human.fasta -T UnifiedGenotyper -I my.bam -L chr1:1-125,000,000 -o my.1.vcf &
gsa1> java -jar GenomeAnalysisTK -R human.fasta -T UnifiedGenotyper -I my.bam -L chr1:125,000,001-249,250,621 -o my.2.vcf &
and wiki posted: "When these two jobs finish, I just merge the two VCFs together and I've got a complete data set in half the time".
But there are headers in VCF files, how to automatically merge these VCF files? Same problems for BAM file, but I found "MergeSamFiles" in Picard, is it a solution for merging bam files? Will it handle different header files in BAM files?
Second, to specify multiple chro, should I use
-L chr1 chr2 chr3
or
-L chr1
-L chr2
Thanks?
•
written
by
C Shao •
1 answer
the two VCFs can be merged using VCFtools: http://vcftools.sourceforge.net/docs.html#merge
I you want to handle several regions, as far as I know the GATK use this kind of list : http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK#Intervals
Log in to answer this question.
-
Scatter Gather principle by chromosome on Gatk
written by Sushant •
-
Snp Calling Error By Gatk Unifiedgenotyper Program
written by Tonyzeng •
-
Base Recalibration Of Stampy Alignments In Gatk
written by jake •
-
Gatk Realignertargetcreator Sam/Bam Header Error
written by Houkto •
-
Gatk Unifiedgenotyper
written by Biostar User •
-
How To Reorder Bam File Contigs For The Gatk Pipeline
written by win
-
A Error About Gatk Samfilereader Malformed
written by huboqiang •
-
Problems In Running Samtools Mpileup/Depth For Specific Regions
written by C Shao •
-
Is It Possible To Split And Merge Bam To Pileup Conversion Process?
written by Prateek
-
Gatk Has Issues With Sorted Bam File
written by Oliver
What kind of computational resources do you have access to? If you have a cluster which is compatible with it you might want to check out using GATK Queue (http://www.broadinstitute.org/gatk/guide/topic?name=tutorials), which can handle scatter/gatter automatically.