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GATK HaplotypeCallerQUAL field changes while running per chromosome

fazulurfazulur hyderabadMember

Dear GATK Team,

I ran GATK haplotypecaller (3.4) on one sample.

  1. In normal procedure . Whole bam file submitted to haplotype caller.
    2 .In another way, BAM was splitted by chromosome ( using -L option) and ran haplotype caller on each chromosome separately and concatenate the per chromosomal vcf's at the end.

I got 2 vcf files and I have observed the changes in INFO and QUAL fields while comparing both.

Does haplotype caller calculates QUAL and INFO fields across all chromosomes?

Please help me to resolve the issue.

Thanks & Regards
Fazulur Rehaman

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