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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

No individual sample info in combineGVCF

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    Genevieve Brandt

    Niyomi House what was your result after CombineGVCFs? Were all 250 samples present? Please also post your commands and stack trace to check for errors.

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    Niyomi House

    Thank you for getting back to me. The CombinedGVCF does not show any individual samples (see attached photo). Usually when I merge files, I see the individual samples after the info column. I've also attached a snippet of the log file (both top and bottom). There are no errors indicating any problems.

    My command is;

    gatk --java-options "-Xmx30G" CombineGVCFs --variant file1.g.vcf.gz --variant file2.g.vcf.gz .... -O cohort.g.vcf.gz 

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    Niyomi House

    Also, does GenotypeGVCFs get rid of all the sites with no calls? (ie: all the sites that have ./. in the cohort.g.vcf are not there after joint genotyping). I couldn't find any information on this anywhere. Thank you in advance. 

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    Genevieve Brandt

    Niyomi House could you please post the entire stack trace so that we can look closer for the error? Some of it is missing in your images above.

    For information about what GenotypeGVCFs is doing, please see this Best Practices Workflow document. GenotypeGVCFs is finding SNP and Indel sites from the GVCF input file.

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