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

Can I continue to run Haplotypecaller when it is broken?



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    Hi Sin Lee

    No you can not. However, since HC is able to operate over regions, you can look into the produced GVCF file and find the last chromosome which was fully and successfully genotyped, e.g. HC was able to genotype chromosomes 1,2,3 and raised an exception while calling chromosome 4. Then you should subset the VCF output for chromosomes 1,2,3 and discard the rest. Then run HC again on the same data but specify -XL chr1 -XL chr2 -XL chr3 (-XL removes the region from analysis) as well as use another name for this new output. Finally, combine the first and the second output via multiple available tools (CombineVariants, for instance).

    -L and -XL options can operate with chromosomal regions like -XL chr1:100-200, however, I do not recommend to use it here for simplicity.

    The most important thing here is to find out the reason for a server error as you say. Besides, GATK4 does not support parallelization in alpha mode (SparkHC is in beta as I recall) which you desperately need to speed up the analysis. I suggest you find out the number of CPUs/threads for your server and run multiple HC commands in parallel (using screen or tmux sessions) per each chromosome. I mean each command should be identical but have a -L argument with chrN value. Then you can combine the produced files using GATK CombineGVCFs. 


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    Bhanu Gandham

    Thank you for your input danilovkiri !!!

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