Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

GATK 4 HaplotypeCaller --intervals, -L usage for non-human genomes

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    Steven Fleck

    I had read that page, but still didn't understand completely. A colleague was able to help out. If anyone else comes to this post for clarification: for two intervals, I needed to submit 2 separate jobs to my cluster:

    gatk --java-options "-Xmx40g" HaplotypeCaller -pairHMM AVX_LOGLESS_CACHING_OMP --native-pair-hmm-threads 32 -L contigs_1_of_2.list -R $ref -I $bam -O gVCF_files/$sampleName.g.vcf -ERC GVCF

    gatk --java-options "-Xmx40g" HaplotypeCaller -pairHMM AVX_LOGLESS_CACHING_OMP --native-pair-hmm-threads 32 -L contigs_2_of_2.list -R $ref -I $bam -O gVCF_files/$sampleName.g.vcf -ERC GVCF

    Where the .list files each contain half of your data worth in contig names. You can combine the .vcf files afterward following the instructions provided by Broad Institute 

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