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variant calling by GATK question about alignment

I have a human whole genome sequence data and I would like to call SNPs/ Indels/ mutations using GATK best practice module. Can I use Bowtie 2 for alignment. Which particular genome I have to use, Does GATK work with GRCH38 or hg19. I have tried to use hg19 as reference genome and GATK gave and error that Bam file does not have right header.

Thanks

alignment gatk
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updated by ijaz786besanttech • ijaz786besanttech • written by rob.costa1234 rob.costa1234

Hello,

I have tried to use hg19 as reference genome and GATK gave and error that Bam file does not have right header.

please provide us the complete error message and the output of samtools view -H yourbamfile.bam.

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