No individual sample info in combineGVCF
c) Why do I see only one sample in my combinedGVCF? I ran Haplotype caller on 250 individual samples under -ERC GVCF (separately for each individual). Then merged them using CombineGVCF and ran the GenotypeGVCFs.
My final VCF is recognized as just ONE sample. Is there a way to merge gvcfs without losing the number of individuals? I can't perform any population genetic analysis with just 1 sample.
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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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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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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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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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