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Running HaplotypeCaller in GATK

I have an issue while running HaplotypeCaller in GATK. This is the entire protocol of what i did:

  1. I have two done whole exome sequencing and i have two sequences (paired ends so forward and reverse). I indexed the human genome using bwa and also aligned the two sequences to it using bwa.
  2. I then sorted the resulting sam file using picard sortsam.
  3. I then wanted to run the haplotypeCaller of gatk on the output bam file to get the vcf file of the available SNVs. But when i run it i get an error: java.lang.IllegalArgumentException: samples cannot be empty.
  4. So i ran picards validatesamfile and this is what i got:

HISTOGRAM java.lang.String

Error Type Count

What does this error mean and how do i solve this? Is there any mistake i am making in my protocol that i should i change in order to not get this error in the future?


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