incomplete or partial VCF file

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Tayebe Ranjbarnejad

• November 17, 2022 08:21

Hello all, I am trying to call germline variants using gatk-4.3.0.0 HaplotypeCaller and Bcftools from one sorted bam file. The generated vcf file of HaplotypeCaller and Bcftools has only variants of chromosomes 10 to 19 and no more. I have also checked the presence aligned reads of other chromosomes in the sorted bam file by IGV.

REQUIRED for all errors and issues:
a) GATK version used:

The Genome Analysis Toolkit (gatk-4.3.0.0(

 
b) Exact command used:

java -jar gatk-package-4.3.0.0-local.jar HaplotypeCaller -I input file address / input file name.bam -O output file address/ output file name.vcf -R reference hg19 file address/hg19.fa

 
c) Entire program log:

No error 

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• 

  Anthony DiCi

  • November 21, 2022 14:19

  Thank you for your post, Tayebe Ranjbarnejad ! I want to let you know we have received your question. We'll get back to you if we have any updates or follow up questions. 

  Please see our Support Policy for more details about how we prioritize responding to questions.

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